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<\/p>\n\u90a3\u6211\u4eec\u8be5\u5982\u4f55\u5feb\u901f\u7684\u5f97\u5230GEO\u6570\u636e\u5e93\u4e2d\u81ea\u5df1\u60f3\u8981\u7684\u6570\u636e\u5462\uff0c\u4eca\u5929\u5c0f\u5e08\u59b9\u5c31\u6765\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e2aR\u5305GEOquery\u5305\uff0cGEOquery\u5305\u662f\u4e00\u4e2aR\u8bed\u8a00\u4e2d\u7684\u751f\u7269\u4fe1\u606f\u5b66\u6570\u636e\u8bfb\u53d6\u5305\uff0c\u53ef\u4ee5\u65b9\u4fbf\u5730\u8bfb\u53d6GEO\u6570\u636e\u5e93\u4e2d\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u3002\u8be5\u5305\u53ef\u4ee5\u8bfb\u53d6GEO\u6570\u636e\u5e93\u4e2d\u7684\u539f\u59cb\u6570\u636e\u548c\u6ce8\u91ca\u4fe1\u606f\uff0c\u652f\u6301\u591a\u79cd\u6570\u636e\u683c\u5f0f\uff0c\u5982CEL\u3001GPR\u3001TXT\u3001CSV\u7b49\uff0c\u53ef\u4ee5\u5feb\u901f\u8bfb\u53d6\u5927\u91cf\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\uff0c\u652f\u6301\u6570\u636e\u9884\u5904\u7406\u3001\u8d28\u91cf\u63a7\u5236\u548c\u7edf\u8ba1\u5206\u6790\u7b49\u529f\u80fd\uff0c\u63d0\u4f9b\u4e86\u4e30\u5bcc\u7684\u6570\u636e\u53ef\u89c6\u5316\u529f\u80fd\u3002<\/p>\n\u90a3\u4e48\u63a5\u4e0b\u6765\u5c31\u7531\u5c0f\u5e08\u59b9\u6765\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e0b\u8fd9\u4e2a\u795e\u5947\u7684R\u5305\u5427\u3002<\/p>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(189, 216, 245);min-width: 5%;height: auto;padding: 6px 15px;\">\n<section style=\"color: rgb(255, 255, 255);text-align: justify;\" powered-by=\"xiumi.us\">\n\u4e00<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: -6px;transform: scale(0.66);transform-origin: left top;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1;transform: translate3d(12px, 0px, 0px);\">\n<section style=\"width: 0px;display: inline-block;border-top: 0.6em solid rgb(247, 221, 223);border-left: 0.6em solid rgb(247, 221, 223);border-bottom: 0.6em solid transparent !important;border-right: 0.6em solid transparent !important;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 100 100 0%;height: auto;align-self: flex-start;background-color: rgb(255, 229, 231);padding: 6px 6px 6px 14px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n\u5b89\u88c5\u548c\u8f7d\u5165<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>\u5b89\u88c5\uff1aif<\/span> (!requireNamespace(\"BiocManager\"<\/span>, quietly=TRUE<\/span>))<\/span><\/code><code> install.packages(\"BiocManager\"<\/span>)<\/span><\/code><code>BiocManager::install(\"GEOquery\"<\/span>)<\/span><\/code><code> <\/span><\/code><code>\u8f7d\u5165\uff1alibrary(GEOquery)<\/span><\/code><\/pre>\n<\/section>\n <\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(189, 216, 245);min-width: 5%;height: auto;padding: 6px 15px;\">\n<section style=\"color: rgb(255, 255, 255);text-align: justify;\" powered-by=\"xiumi.us\">\n\u4e8c<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: -6px;transform: scale(0.66);transform-origin: left top;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1;transform: translate3d(12px, 0px, 0px);\">\n<section style=\"width: 0px;display: inline-block;border-top: 0.6em solid rgb(247, 221, 223);border-left: 0.6em solid rgb(247, 221, 223);border-bottom: 0.6em solid transparent !important;border-right: 0.6em solid transparent !important;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 100 100 0%;height: auto;align-self: flex-start;background-color: rgb(255, 229, 231);padding: 6px 6px 6px 14px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n\u76f8\u5173\u64cd\u4f5c<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n1. GEOquery \u83b7\u53d6\u6570\u636e<\/strong><\/p>\ngetGEO\uff0c\u8fd9\u4e00\u4e2a\u547d\u4ee4\u5c31\u53ef\u4ee5\u8ba9\u6211\u4eec\u4ece GEO \u4e2d\u83b7\u53d6\u6570\u636e\uff0c\u5e38\u7528\u7684\u65b9\u5f0f\u662f\u4f20\u5165 GEO accession\uff0c\u5c0f\u5e08\u59b9\u6765\u4e3e\u4e2a\u4f8b\u5b50\uff1a<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>> gds <- getGEO(filename=system.file(\"extdata\/GDS507.soft.gz\"<\/span>,package=\"GEOquery\"<\/span>))<\/span><\/code><code>>gsm <- getGEO(filename=system.file(\"extdata\/GSM11805.txt.gz\"<\/span>,package=\"GEOquery\"<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.2934472934472934\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_JIkTmukTNiatWfHUwGNvQ3umxjic2Q-4.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX9957rhWSrDbtLCBYnqsiaiaKtSqADbTUia7UYpfjALP3HzVgfvJIkTmukTNiatWfHUwGNvQ3umxjic2Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"702\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n\u5982\u56fe\u6240\u793a\uff0c\u73b0\u5728gds \u5305\u542b\u4e86 R \u6570\u636e\u7ed3\u6784(GDS \u7c7b)\uff0c\u8868\u793a GEO \u7684 GDS507 \u6761\u76ee\u3002<\/p>\n <\/p>\n2.getGEO\u4ecb\u7ecd<\/strong><\/p>\ngetGEO\u662fR\u8bed\u8a00\u4e2dGEOquery\u5305\u63d0\u4f9b\u7684\u4e00\u4e2a\u51fd\u6570\uff0c\u7528\u4e8e\u4eceGEO\u6570\u636e\u5e93\u4e2d\u4e0b\u8f7d\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u3002\u4f7f\u7528getGEO\u51fd\u6570\u53ef\u4ee5\u65b9\u4fbf\u5730\u83b7\u53d6GEO\u6570\u636e\u5e93\u4e2d\u7684\u6570\u636e\uff0c\u5e76\u5c06\u6570\u636e\u5b58\u50a8\u4e3aR\u8bed\u8a00\u4e2d\u7684\u5bf9\u8c61\uff0c\u4ee5\u4fbf\u8fdb\u884c\u540e\u7eed\u7684\u5206\u6790\u548c\u5904\u7406\u3002<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>getGEO(GEO, destdir = \".\"<\/span>, AnnotGPL = FALSE<\/span>, getGPL = TRUE<\/span>, GSEMatrix = FALSE<\/span>, AnnotGSE = FALSE<\/span>, verbose = TRUE<\/span>)<\/span><\/code><\/pre>\n<\/section>\n <\/p>\n3.GEOquery \u7684\u6570\u636e\u7ed3\u6784<\/strong><\/p>\n<section powered-by=\"xiumi.us\">\nGEOquery\u5305\u4e2d\u7684\u6570\u636e\u7ed3\u6784\u4e3b\u8981\u5305\u62ecGSE\u3001GSM\u3001GDS\u548cGPL\u56db\u79cd\u7c7b\u578b\uff0c\u5206\u522b\u5bf9\u5e94GEO\u6570\u636e\u5e93\u4e2d\u7684\u5b9e\u9a8c\u96c6\u3001\u6837\u672c\u3001\u6570\u636e\u96c6\u548c\u82af\u7247\u5e73\u53f0\u3002<\/p>\n\uff081\uff09GSM\uff08Gene Expression Sample\uff09\uff1aGSM\u662fGEO\u6570\u636e\u5e93\u4e2d\u7684\u6837\u672c\uff0c\u5bf9\u5e94\u4e8e\u5b9e\u9a8c\u96c6\u4e2d\u7684\u6bcf\u4e2a\u6837\u672c\u3002\u5728GEOquery\u4e2d\uff0cGSM\u6570\u636e\u7ed3\u6784\u662f\u4e00\u4e2a\u6570\u636e\u6846\uff0c\u5305\u542b\u4e86\u6837\u672c\u7684\u6ce8\u91ca\u4fe1\u606f\u548c\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u3002<\/p>\n\uff082\uff09GDS\uff08Gene Expression Dataset\uff09\uff1aGDS\u662fGEO\u6570\u636e\u5e93\u4e2d\u7684\u6570\u636e\u96c6\uff0c\u5305\u542b\u4e86\u591a\u4e2a\u6837\u672c\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u3002\u5728GEOquery\u4e2d\uff0cGDS\u6570\u636e\u7ed3\u6784\u662f\u4e00\u4e2a\u5217\u8868\uff0c\u5305\u542b\u4e86\u6570\u636e\u96c6\u7684\u6ce8\u91ca\u4fe1\u606f\u548c\u6bcf\u4e2a\u6837\u672c\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u77e9\u9635\u3002<\/p>\n\uff083\uff09GPL\uff08Gene Expression Platform\uff09\uff1aGPL\u662fGEO\u6570\u636e\u5e93\u4e2d\u7684\u82af\u7247\u5e73\u53f0\uff0c\u5305\u542b\u4e86\u82af\u7247\u4e0a\u63a2\u9488\u7684\u6ce8\u91ca\u4fe1\u606f\u548c\u5e8f\u5217\u4fe1\u606f\u3002\u5728GEOquery\u4e2d\uff0cGPL\u6570\u636e\u7ed3\u6784\u662f\u4e00\u4e2a\u6570\u636e\u6846\uff0c\u5305\u542b\u4e86\u82af\u7247\u5e73\u53f0\u7684\u6ce8\u91ca\u4fe1\u606f\u548c\u63a2\u9488\u5e8f\u5217\u4fe1\u606f\u3002<\/p>\n\uff084\uff09GSE\uff08Gene Expression Series\uff09\uff1aGSE\u662fGEO\u6570\u636e\u5e93\u4e2d\u7684\u5b9e\u9a8c\u96c6\uff0c\u5305\u62ec\u591a\u4e2a\u6837\u672c\u548c\u5176\u5bf9\u5e94\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u3002\u5728GEOquery\u4e2d\uff0cGSE\u6570\u636e\u7ed3\u6784\u662f\u4e00\u4e2a\u5217\u8868\uff0c\u5305\u542b\u4e86\u5b9e\u9a8c\u7684\u6ce8\u91ca\u4fe1\u606f\u548c\u6bcf\u4e2a\u6837\u672c\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u77e9\u9635\u3002<\/p>\n<\/section>\n <\/p>\n<section powered-by=\"xiumi.us\">\n\u4e0b\u9762\u5c0f\u5e08\u59b9\u5c06\u5bf9\u4ed6\u4eec\u8fdb\u884c\u7b80\u5355\u7684\u4ecb\u7ecd\uff0c\u5e2e\u52a9\u5927\u5bb6\u7406\u89e3\uff0c\u5148\u4ecb\u7ecd\u524d\u4e09\u79cd\u7c7b\u578b\u3002<\/p>\nGSM\u3001GDS\u3001GPL\uff0c\u8fd9\u4e09\u79cd\u7c7b\u578b\uff0c\u6bcf\u4e00\u4e2a\u7c7b\u90fd\u7531\u4e00\u4e2a\u5143\u6570\u636e\u5934\uff08\u4e0e SOFT \u683c\u5f0f\u5934\u90e8\u4fe1\u606f\u51e0\u4e4e\u4e00\u81f4\uff09\u548c\u4e00\u4e2a GEODataTable \u7ec4\u6210\u3002GEODataTable \u6709\u4e24\u4e2a\u7b80\u5355\u7684\u90e8\u5206: Columns \u548c Table\uff0cColumns \u90e8\u5206\u662f\u5bf9 Table \u90e8\u5206\u7684\u5217\u7684\u63cf\u8ff0\u3002\u6b64\u5916\uff0c\u6bcf\u4e2a\u7c7b\u8fd8\u6709\u4e00\u4e2a show \u65b9\u6cd5\u3002\u4f8b\u5982\u6211\u4eec\u5df2\u7ecf\u83b7\u53d6\u7684gsm\u6570\u636e\uff1a<\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>#\u67e5\u770b\u5143\u6570\u636e<\/span><\/span><\/code><code>> head(Meta(gsm))<\/span><\/code><code>$channel_count<\/span><\/code><code>[1<\/span>] \"1\"<\/span><\/span><\/code><code>$comment<\/span><\/code><code>[1<\/span>] \"Raw data provided as supplementary file\"<\/span><\/span><\/code><code>$contact_address<\/span><\/code><code>[1<\/span>] \"715 Albany Street, E613B\"<\/span><\/span><\/code><code>$contact_city<\/span><\/code><code>[1<\/span>] \"Boston\"<\/span><\/span><\/code><code>$contact_country<\/span><\/code><code>[1<\/span>] \"USA\"<\/span><\/span><\/code><code>$contact_department<\/span><\/code><code>[1<\/span>]\"Genetics and Genomics\"<\/span><\/span><\/code><code> <\/span><\/code><code>#\u67e5\u770b\u4e0e GSM \u76f8\u5173\u7684\u6570\u636e<\/span><\/span><\/code><code>> Table(gsm)[1<\/span>:8<\/span>,] ID_REF VALUE ABS_CALL<\/span><\/code><code>1<\/span> AFFX-BioB-5<\/span>_at 953.9<\/span> P<\/span><\/code><code>2<\/span> AFFX-BioB-M_at 2982.8<\/span> P<\/span><\/code><code>3<\/span> AFFX-BioB-3<\/span>_at 1657.9<\/span> P<\/span><\/code><code>4<\/span> AFFX-BioC-5<\/span>_at 2652.7<\/span> P<\/span><\/code><code>5<\/span> AFFX-BioC-3<\/span>_at 2019.5<\/span> P<\/span><\/code><code>6<\/span> AFFX-BioDn-5<\/span>_at 3531.5<\/span> P<\/span><\/code><code>7<\/span> AFFX-BioDn-3<\/span>_at 14950.5<\/span> P<\/span><\/code><code>8<\/span> AFFX-CreX-5<\/span>_at 27206.6<\/span> P<\/span><\/code><code> <\/span><\/code><code>#\u67e5\u770b\u5217\u63cf\u8ff0<\/span><\/span><\/code><code>> Columns(gsm)<\/span><\/code><code> Column Description<\/span><\/code><code>1<\/span> ID_REF <\/span><\/code><code>2<\/span> VALUE MAS 5.0<\/span> Statistical Algorithm (mean scaled to 500<\/span>)<\/span><\/code><code>3<\/span> ABS_CALL MAS 5.0<\/span> Absent, Marginal, Present call<\/span> with Alpha1 = 0.05<\/span>, Alpha2 = 0.065<\/span><\/span><\/code><\/pre>\n<\/section>\n <\/p>\n\u800cGSE \u6709\u4e00\u4e2a\u5143\u6570\u636e\u90e8\u5206\uff0c\u4f46\u5b83\u6ca1\u6709 GEODataTable\uff0c\u5b83\u5305\u542b\u4e86\u4e24\u4e2a\u5217\u8868\uff0c\u53ef\u4ee5\u4f7f\u7528 GPLList \u548c GSMList \u65b9\u6cd5\u8fdb\u884c\u8bbf\u95ee\uff0c\u8fd9\u4e24\u4e2a\u5217\u8868\u5206\u522b\u662f GPL \u548c GSM \u5bf9\u8c61\u7684\u5217\u8868\u3002\u5c0f\u5e08\u59b9\u62ffsoft \u6587\u4ef6\u6765\u4e3e\u4e2a\u4f8b\u5b50\uff1a<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>> gse <- getGEO(filename=system.file(\"extdata\/GSE781_family.soft.gz\"<\/span>,package=\"GEOquery\"<\/span>))<\/span><\/code><code>#\u67e5\u770b\u5143\u6570\u636e<\/span><\/span><\/code><code>> head(Meta(gse))$contact_address<\/span><\/code><code>[1<\/span>] \"715 Albany Street, E613B\"<\/span><\/span><\/code><code>$contact_city<\/span><\/code><code>[1<\/span>] \"Boston\"<\/span><\/span><\/code><code>$contact_country<\/span><\/code><code>[1<\/span>] \"USA\"<\/span><\/span><\/code><code>$contact_department<\/span><\/code><code>[1<\/span>] \"Genetics and Genomics\"<\/span><\/span><\/code><code>$contact_email<\/span><\/code><code>[1<\/span>] \"mlenburg@bu.edu\"<\/span><\/span><\/code><code>$contact_fax<\/span><\/code><code>[1<\/span>]\"617-414-1646\"<\/span><\/span><\/code><code> <\/span><\/code><code>#\u83b7\u53d6 GSE \u4e2d\u5305\u542b\u7684\u6240\u6709 GSM \u5bf9\u8c61\u7684\u540d\u79f0<\/span><\/span><\/code><code>> names<\/span>(GSMList(gse)) [1<\/span>] \"GSM11805\"<\/span> \"GSM11810\"<\/span> \"GSM11814\"<\/span> \"GSM11815\"<\/span> \"GSM11823\"<\/span> \"GSM11827\"<\/span> \"GSM11830\"<\/span> \"GSM11832\"<\/span><\/span><\/code><code> [9<\/span>] \"GSM12067\"<\/span> \"GSM12069\"<\/span> \"GSM12075\"<\/span> \"GSM12078\"<\/span> \"GSM12079\"<\/span> \"GSM12083\"<\/span> \"GSM12098\"<\/span> \"GSM12099\"<\/span><\/span><\/code><code>[17<\/span>] \"GSM12100\"<\/span> \"GSM12101\"<\/span> \"GSM12105\"<\/span> \"GSM12106\"<\/span> \"GSM12268\"<\/span> \"GSM12269\"<\/span> \"GSM12270\"<\/span> \"GSM12274\"<\/span><\/span><\/code><code>[25<\/span>] \"GSM12283\"<\/span> \"GSM12287\"<\/span> \"GSM12298\"<\/span> \"GSM12299\"<\/span> \"GSM12300\"<\/span> \"GSM12301\"<\/span> \"GSM12399\"<\/span> \"GSM12412\"<\/span><\/span><\/code><code>[33<\/span>] \"GSM12444\"<\/span> \"GSM12448\"<\/span><\/span><\/code><code> <\/span><\/code><code>#\u83b7\u5f97\u5217\u8868\u4e2d\u7684\u7b2c\u4e00\u4e2a GSM \u5bf9\u8c61<\/span><\/span><\/code><code>> GSMList(gse)[[1<\/span>]]An object of class<\/span> \"GSM\"<\/span><\/span><\/code><code>channel_count <\/span><\/code><code>[1<\/span>] \"1\"<\/span><\/span><\/code><code>comment <\/span><\/code><code>[1<\/span>] \"Raw data provided as supplementary file\"<\/span><\/span><\/code><code>contact_address <\/span><\/code><code>[1<\/span>] \"715 Albany Street, E613B\"<\/span><\/span><\/code><code>contact_city <\/span><\/code><code>[1<\/span>] \"Boston\"<\/span><\/span><\/code><code>contact_country <\/span><\/code><code>[1<\/span>] \"USA\"<\/span><\/span><\/code><code>contact_department <\/span><\/code><code>[1<\/span>] \"Genetics and Genomics\"<\/span><\/span><\/code><code>contact_email <\/span><\/code><code>[1<\/span>] \"mlenburg@bu.edu\"<\/span><\/span><\/code><code>contact_fax <\/span><\/code><code>[1<\/span>] \"617-414-1646\"<\/span><\/span><\/code><code>contact_institute <\/span><\/code><code>[1<\/span>] \"Boston University School of Medicine\"<\/span><\/span><\/code><code>contact_name <\/span><\/code><code>[1<\/span>] \"Marc,E.,Lenburg\"<\/span><\/span><\/code><code>contact_phone <\/span><\/code><code>[1<\/span>] \"617-414-1375\"<\/span><\/span><\/code><code>contact_state <\/span><\/code><code>[1<\/span>] \"MA\"<\/span><\/span><\/code><code>contact_web_link <\/span><\/code><code>[1<\/span>] \"http:\/\/gg.bu.edu\"<\/span><\/span><\/code><code>contact_zip\/postal_code <\/span><\/code><code>[1<\/span>] \"02130\"<\/span><\/span><\/code><code>data_row_count <\/span><\/code><code>[1<\/span>] \"22283\"<\/span><\/span><\/code><code>description <\/span><\/code><code>[1<\/span>] \"Age = 70; Gender = Female; Right Kidney; Adjacent Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 3; Adjacent Tumor Capsule Penetration = true; Adjacent Tumor Perinephric Fat Invasion = true; Adjacent Tumor Renal Sinus Invasion = false; Adjacent Tumor Renal Vein Invasion = true; Scaling Target = 500; Scaling Factor = 7.09; Raw Q = 2.39; Noise = 2.60; Background = 55.24.\"<\/span><\/span><\/code><code>[2<\/span>] \"Keywords = kidney\"<\/span> [3<\/span>] \"Keywords = renal\"<\/span> <\/span><\/code><code>[4<\/span>] \"Keywords = RCC\"<\/span> <\/span><\/code><code>[5<\/span>] \"Keywords = carcinoma\"<\/span> <\/span><\/code><code>[6<\/span>] \"Keywords = cancer\"<\/span> [7<\/span>] \"Lot batch = 2004638\"<\/span> <\/span><\/code><code>geo_accession <\/span><\/code><code>[1<\/span>] \"GSM11805\"<\/span><\/span><\/code><code>last_update_date <\/span><\/code><code>[1<\/span>] \"May 28 2005\"<\/span><\/span><\/code><code>molecule_ch1 <\/span><\/code><code>[1<\/span>] \"total RNA\"<\/span><\/span><\/code><code>organism_ch1 <\/span><\/code><code>[1<\/span>] \"Homo sapiens\"<\/span><\/span><\/code><code>platform_id <\/span><\/code><code>[1<\/span>] \"GPL96\"<\/span><\/span><\/code><code>series_id <\/span><\/code><code>[1<\/span>] \"GSE781\"<\/span><\/span><\/code><code>source_name_ch1 <\/span><\/code><code>[1<\/span>] \"Trizol isolation of total RNA from normal tissue adjacent to Renal Cell Carcinoma\"<\/span><\/span><\/code><code>status <\/span><\/code><code>[1<\/span>] \"Public on Nov 25 2003\"<\/span><\/span><\/code><code>submission_date <\/span><\/code><code>[1<\/span>] \"Oct 20 2003\"<\/span><\/span><\/code><code>supplementary_file <\/span><\/code><code>[1<\/span>] \"ftp:\/\/ftp.ncbi.nih.gov\/pub\/geo\/DATA\/supplementary\/samples\/GSM11nnn\/GSM11805\/GSM11805.CEL.gz\"<\/span><\/span><\/code><code>title <\/span><\/code><code>[1<\/span>] \"N035 Normal Human Kidney U133A\"<\/span><\/span><\/code><code>type <\/span><\/code><code>[1<\/span>] \"RNA\"<\/span><\/span><\/code><code>An object of class<\/span> \"GEODataTable\"<\/span><\/span><\/code><code>****** Column Descriptions ******<\/span><\/code><code> Column Description<\/span><\/code><code>1<\/span> ID_REF =<\/span><\/code><code>2<\/span> VALUE MAS 5.0<\/span> Statistical Algorithm (mean scaled to 500<\/span>)<\/span><\/code><code>3<\/span> 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powered-by=\"xiumi.us\">\n\u4e86\u89e3\u751f\u4fe1\u7684\u5c0f\u4f19\u4f34\u5e94\u8be5\u90fd\u77e5\u9053GEO\u6570\u636e\u5e93\uff0c\u5b83\u662f\u751f\u7269\u4fe1\u606f\u5b66\u7814\u7a76\u4e2d\u5e38\u7528\u7684\u6570\u636e\u8d44\u6e90\u4e4b\u4e00\u3002GEO\u6570\u636e\u5e93\u4e2d\u7684\u6570\u636e\u4e3b\u8981\u6765\u6e90\u4e8e\u9ad8\u901a\u91cf\u57fa\u56e0\u8868\u8fbe\u5b9e\u9a8c\uff0c\u5982\u57fa\u56e0\u82af\u7247\u548cRNA\u6d4b\u5e8f\u7b49\u3002\u8fd9\u4e9b\u6570\u636e\u53ef\u4ee5\u7528\u6765\u7814\u7a76\u57fa\u56e0\u8c03\u63a7\u3001\u751f\u7269\u8fdb\u5316\u3001\u75be\u75c5\u53d1\u751f\u673a\u5236\u7b49\u751f\u7269\u5b66\u95ee\u9898\u3002GEO\u6570\u636e\u5e93\u4e2d\u7684\u6570\u636e\u901a\u5e38\u5305\u62ec\u539f\u59cb\u6570\u636e\u548c\u6ce8\u91ca\u4fe1\u606f\uff0c\u539f\u59cb\u6570\u636e\u53ef\u4ee5\u901a\u8fc7\u751f\u7269\u4fe1\u606f\u5b66\u5de5\u5177\u8fdb\u884c\u9884\u5904\u7406\u548c\u5206\u6790\uff0c\u6ce8\u91ca\u4fe1\u606f\u5305\u62ec\u6837\u672c\u4fe1\u606f\u3001\u5b9e\u9a8c\u8bbe\u8ba1\u3001\u57fa\u56e0\u6ce8\u91ca\u7b49\uff0c\u53ef\u4ee5\u5e2e\u52a9\u7814\u7a76\u8005\u7406\u89e3\u6570\u636e\u7684\u6765\u6e90\u548c\u7279\u70b9\u3002<\/span> <\/p>\n\u90a3\u6211\u4eec\u8be5\u5982\u4f55\u5feb\u901f\u7684\u5f97\u5230GEO\u6570\u636e\u5e93\u4e2d\u81ea\u5df1\u60f3\u8981\u7684\u6570\u636e\u5462\uff0c\u4eca\u5929\u5c0f\u5e08\u59b9\u5c31\u6765\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e2aR\u5305GEOquery\u5305\uff0cGEOquery\u5305\u662f\u4e00\u4e2aR\u8bed\u8a00\u4e2d\u7684\u751f\u7269\u4fe1\u606f\u5b66\u6570\u636e\u8bfb\u53d6\u5305\uff0c\u53ef\u4ee5\u65b9\u4fbf\u5730\u8bfb\u53d6GEO\u6570\u636e\u5e93\u4e2d\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u3002\u8be5\u5305\u53ef\u4ee5\u8bfb\u53d6GEO\u6570\u636e\u5e93\u4e2d\u7684\u539f\u59cb\u6570\u636e\u548c\u6ce8\u91ca\u4fe1\u606f\uff0c\u652f\u6301\u591a\u79cd\u6570\u636e\u683c\u5f0f\uff0c\u5982CEL\u3001GPR\u3001TXT\u3001CSV\u7b49\uff0c\u53ef\u4ee5\u5feb\u901f\u8bfb\u53d6\u5927\u91cf\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\uff0c\u652f\u6301\u6570\u636e\u9884\u5904\u7406\u3001\u8d28\u91cf\u63a7\u5236\u548c\u7edf\u8ba1\u5206\u6790\u7b49\u529f\u80fd\uff0c\u63d0\u4f9b\u4e86\u4e30\u5bcc\u7684\u6570\u636e\u53ef\u89c6\u5316\u529f\u80fd\u3002<\/p>\n\u90a3\u4e48\u63a5\u4e0b\u6765\u5c31\u7531\u5c0f\u5e08\u59b9\u6765\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e0b\u8fd9\u4e2a\u795e\u5947\u7684R\u5305\u5427\u3002<\/p>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(189, 216, 245);min-width: 5%;height: auto;padding: 6px 15px;\">\n<section style=\"color: rgb(255, 255, 255);text-align: justify;\" powered-by=\"xiumi.us\">\n\u4e00<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: -6px;transform: scale(0.66);transform-origin: left top;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1;transform: translate3d(12px, 0px, 0px);\">\n<section style=\"width: 0px;display: inline-block;border-top: 0.6em solid rgb(247, 221, 223);border-left: 0.6em solid rgb(247, 221, 223);border-bottom: 0.6em solid transparent !important;border-right: 0.6em solid transparent !important;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 100 100 0%;height: auto;align-self: flex-start;background-color: rgb(255, 229, 231);padding: 6px 6px 6px 14px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n\u5b89\u88c5\u548c\u8f7d\u5165<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>\u5b89\u88c5\uff1aif<\/span> (!requireNamespace(\"BiocManager\"<\/span>, quietly=TRUE<\/span>))<\/span><\/code><code> install.packages(\"BiocManager\"<\/span>)<\/span><\/code><code>BiocManager::install(\"GEOquery\"<\/span>)<\/span><\/code><code> <\/span><\/code><code>\u8f7d\u5165\uff1alibrary(GEOquery)<\/span><\/code><\/pre>\n<\/section>\n <\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(189, 216, 245);min-width: 5%;height: auto;padding: 6px 15px;\">\n<section style=\"color: rgb(255, 255, 255);text-align: justify;\" powered-by=\"xiumi.us\">\n\u4e8c<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: -6px;transform: scale(0.66);transform-origin: left top;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1;transform: translate3d(12px, 0px, 0px);\">\n<section style=\"width: 0px;display: inline-block;border-top: 0.6em solid rgb(247, 221, 223);border-left: 0.6em solid rgb(247, 221, 223);border-bottom: 0.6em solid transparent !important;border-right: 0.6em solid transparent !important;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 100 100 0%;height: auto;align-self: flex-start;background-color: rgb(255, 229, 231);padding: 6px 6px 6px 14px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n\u76f8\u5173\u64cd\u4f5c<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n1. GEOquery \u83b7\u53d6\u6570\u636e<\/strong><\/p>\ngetGEO\uff0c\u8fd9\u4e00\u4e2a\u547d\u4ee4\u5c31\u53ef\u4ee5\u8ba9\u6211\u4eec\u4ece GEO \u4e2d\u83b7\u53d6\u6570\u636e\uff0c\u5e38\u7528\u7684\u65b9\u5f0f\u662f\u4f20\u5165 GEO accession\uff0c\u5c0f\u5e08\u59b9\u6765\u4e3e\u4e2a\u4f8b\u5b50\uff1a<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>> gds <- getGEO(filename=system.file(\"extdata\/GDS507.soft.gz\"<\/span>,package=\"GEOquery\"<\/span>))<\/span><\/code><code>>gsm <- getGEO(filename=system.file(\"extdata\/GSM11805.txt.gz\"<\/span>,package=\"GEOquery\"<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.2934472934472934\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_JIkTmukTNiatWfHUwGNvQ3umxjic2Q-4.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX9957rhWSrDbtLCBYnqsiaiaKtSqADbTUia7UYpfjALP3HzVgfvJIkTmukTNiatWfHUwGNvQ3umxjic2Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"702\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n\u5982\u56fe\u6240\u793a\uff0c\u73b0\u5728gds \u5305\u542b\u4e86 R \u6570\u636e\u7ed3\u6784(GDS \u7c7b)\uff0c\u8868\u793a GEO \u7684 GDS507 \u6761\u76ee\u3002<\/p>\n <\/p>\n2.getGEO\u4ecb\u7ecd<\/strong><\/p>\ngetGEO\u662fR\u8bed\u8a00\u4e2dGEOquery\u5305\u63d0\u4f9b\u7684\u4e00\u4e2a\u51fd\u6570\uff0c\u7528\u4e8e\u4eceGEO\u6570\u636e\u5e93\u4e2d\u4e0b\u8f7d\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u3002\u4f7f\u7528getGEO\u51fd\u6570\u53ef\u4ee5\u65b9\u4fbf\u5730\u83b7\u53d6GEO\u6570\u636e\u5e93\u4e2d\u7684\u6570\u636e\uff0c\u5e76\u5c06\u6570\u636e\u5b58\u50a8\u4e3aR\u8bed\u8a00\u4e2d\u7684\u5bf9\u8c61\uff0c\u4ee5\u4fbf\u8fdb\u884c\u540e\u7eed\u7684\u5206\u6790\u548c\u5904\u7406\u3002<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>getGEO(GEO, destdir = \".\"<\/span>, AnnotGPL = FALSE<\/span>, getGPL = TRUE<\/span>, GSEMatrix = FALSE<\/span>, AnnotGSE = FALSE<\/span>, verbose = TRUE<\/span>)<\/span><\/code><\/pre>\n<\/section>\n <\/p>\n3.GEOquery \u7684\u6570\u636e\u7ed3\u6784<\/strong><\/p>\n<section powered-by=\"xiumi.us\">\nGEOquery\u5305\u4e2d\u7684\u6570\u636e\u7ed3\u6784\u4e3b\u8981\u5305\u62ecGSE\u3001GSM\u3001GDS\u548cGPL\u56db\u79cd\u7c7b\u578b\uff0c\u5206\u522b\u5bf9\u5e94GEO\u6570\u636e\u5e93\u4e2d\u7684\u5b9e\u9a8c\u96c6\u3001\u6837\u672c\u3001\u6570\u636e\u96c6\u548c\u82af\u7247\u5e73\u53f0\u3002<\/p>\n\uff081\uff09GSM\uff08Gene Expression Sample\uff09\uff1aGSM\u662fGEO\u6570\u636e\u5e93\u4e2d\u7684\u6837\u672c\uff0c\u5bf9\u5e94\u4e8e\u5b9e\u9a8c\u96c6\u4e2d\u7684\u6bcf\u4e2a\u6837\u672c\u3002\u5728GEOquery\u4e2d\uff0cGSM\u6570\u636e\u7ed3\u6784\u662f\u4e00\u4e2a\u6570\u636e\u6846\uff0c\u5305\u542b\u4e86\u6837\u672c\u7684\u6ce8\u91ca\u4fe1\u606f\u548c\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u3002<\/p>\n\uff082\uff09GDS\uff08Gene Expression Dataset\uff09\uff1aGDS\u662fGEO\u6570\u636e\u5e93\u4e2d\u7684\u6570\u636e\u96c6\uff0c\u5305\u542b\u4e86\u591a\u4e2a\u6837\u672c\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u3002\u5728GEOquery\u4e2d\uff0cGDS\u6570\u636e\u7ed3\u6784\u662f\u4e00\u4e2a\u5217\u8868\uff0c\u5305\u542b\u4e86\u6570\u636e\u96c6\u7684\u6ce8\u91ca\u4fe1\u606f\u548c\u6bcf\u4e2a\u6837\u672c\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u77e9\u9635\u3002<\/p>\n\uff083\uff09GPL\uff08Gene Expression Platform\uff09\uff1aGPL\u662fGEO\u6570\u636e\u5e93\u4e2d\u7684\u82af\u7247\u5e73\u53f0\uff0c\u5305\u542b\u4e86\u82af\u7247\u4e0a\u63a2\u9488\u7684\u6ce8\u91ca\u4fe1\u606f\u548c\u5e8f\u5217\u4fe1\u606f\u3002\u5728GEOquery\u4e2d\uff0cGPL\u6570\u636e\u7ed3\u6784\u662f\u4e00\u4e2a\u6570\u636e\u6846\uff0c\u5305\u542b\u4e86\u82af\u7247\u5e73\u53f0\u7684\u6ce8\u91ca\u4fe1\u606f\u548c\u63a2\u9488\u5e8f\u5217\u4fe1\u606f\u3002<\/p>\n\uff084\uff09GSE\uff08Gene Expression Series\uff09\uff1aGSE\u662fGEO\u6570\u636e\u5e93\u4e2d\u7684\u5b9e\u9a8c\u96c6\uff0c\u5305\u62ec\u591a\u4e2a\u6837\u672c\u548c\u5176\u5bf9\u5e94\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u3002\u5728GEOquery\u4e2d\uff0cGSE\u6570\u636e\u7ed3\u6784\u662f\u4e00\u4e2a\u5217\u8868\uff0c\u5305\u542b\u4e86\u5b9e\u9a8c\u7684\u6ce8\u91ca\u4fe1\u606f\u548c\u6bcf\u4e2a\u6837\u672c\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u77e9\u9635\u3002<\/p>\n<\/section>\n <\/p>\n<section powered-by=\"xiumi.us\">\n\u4e0b\u9762\u5c0f\u5e08\u59b9\u5c06\u5bf9\u4ed6\u4eec\u8fdb\u884c\u7b80\u5355\u7684\u4ecb\u7ecd\uff0c\u5e2e\u52a9\u5927\u5bb6\u7406\u89e3\uff0c\u5148\u4ecb\u7ecd\u524d\u4e09\u79cd\u7c7b\u578b\u3002<\/p>\nGSM\u3001GDS\u3001GPL\uff0c\u8fd9\u4e09\u79cd\u7c7b\u578b\uff0c\u6bcf\u4e00\u4e2a\u7c7b\u90fd\u7531\u4e00\u4e2a\u5143\u6570\u636e\u5934\uff08\u4e0e SOFT \u683c\u5f0f\u5934\u90e8\u4fe1\u606f\u51e0\u4e4e\u4e00\u81f4\uff09\u548c\u4e00\u4e2a GEODataTable \u7ec4\u6210\u3002GEODataTable \u6709\u4e24\u4e2a\u7b80\u5355\u7684\u90e8\u5206: Columns \u548c Table\uff0cColumns \u90e8\u5206\u662f\u5bf9 Table \u90e8\u5206\u7684\u5217\u7684\u63cf\u8ff0\u3002\u6b64\u5916\uff0c\u6bcf\u4e2a\u7c7b\u8fd8\u6709\u4e00\u4e2a show \u65b9\u6cd5\u3002\u4f8b\u5982\u6211\u4eec\u5df2\u7ecf\u83b7\u53d6\u7684gsm\u6570\u636e\uff1a<\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>#\u67e5\u770b\u5143\u6570\u636e<\/span><\/span><\/code><code>> head(Meta(gsm))<\/span><\/code><code>$channel_count<\/span><\/code><code>[1<\/span>] \"1\"<\/span><\/span><\/code><code>$comment<\/span><\/code><code>[1<\/span>] \"Raw data provided as supplementary file\"<\/span><\/span><\/code><code>$contact_address<\/span><\/code><code>[1<\/span>] \"715 Albany Street, E613B\"<\/span><\/span><\/code><code>$contact_city<\/span><\/code><code>[1<\/span>] \"Boston\"<\/span><\/span><\/code><code>$contact_country<\/span><\/code><code>[1<\/span>] \"USA\"<\/span><\/span><\/code><code>$contact_department<\/span><\/code><code>[1<\/span>]\"Genetics and Genomics\"<\/span><\/span><\/code><code> <\/span><\/code><code>#\u67e5\u770b\u4e0e GSM \u76f8\u5173\u7684\u6570\u636e<\/span><\/span><\/code><code>> Table(gsm)[1<\/span>:8<\/span>,] ID_REF VALUE ABS_CALL<\/span><\/code><code>1<\/span> AFFX-BioB-5<\/span>_at 953.9<\/span> P<\/span><\/code><code>2<\/span> AFFX-BioB-M_at 2982.8<\/span> P<\/span><\/code><code>3<\/span> AFFX-BioB-3<\/span>_at 1657.9<\/span> P<\/span><\/code><code>4<\/span> AFFX-BioC-5<\/span>_at 2652.7<\/span> P<\/span><\/code><code>5<\/span> AFFX-BioC-3<\/span>_at 2019.5<\/span> P<\/span><\/code><code>6<\/span> AFFX-BioDn-5<\/span>_at 3531.5<\/span> P<\/span><\/code><code>7<\/span> AFFX-BioDn-3<\/span>_at 14950.5<\/span> P<\/span><\/code><code>8<\/span> AFFX-CreX-5<\/span>_at 27206.6<\/span> P<\/span><\/code><code> <\/span><\/code><code>#\u67e5\u770b\u5217\u63cf\u8ff0<\/span><\/span><\/code><code>> Columns(gsm)<\/span><\/code><code> Column Description<\/span><\/code><code>1<\/span> ID_REF <\/span><\/code><code>2<\/span> VALUE MAS 5.0<\/span> Statistical Algorithm (mean scaled to 500<\/span>)<\/span><\/code><code>3<\/span> ABS_CALL MAS 5.0<\/span> Absent, Marginal, Present call<\/span> with Alpha1 = 0.05<\/span>, Alpha2 = 0.065<\/span><\/span><\/code><\/pre>\n<\/section>\n <\/p>\n\u800cGSE \u6709\u4e00\u4e2a\u5143\u6570\u636e\u90e8\u5206\uff0c\u4f46\u5b83\u6ca1\u6709 GEODataTable\uff0c\u5b83\u5305\u542b\u4e86\u4e24\u4e2a\u5217\u8868\uff0c\u53ef\u4ee5\u4f7f\u7528 GPLList \u548c GSMList \u65b9\u6cd5\u8fdb\u884c\u8bbf\u95ee\uff0c\u8fd9\u4e24\u4e2a\u5217\u8868\u5206\u522b\u662f GPL \u548c GSM \u5bf9\u8c61\u7684\u5217\u8868\u3002\u5c0f\u5e08\u59b9\u62ffsoft \u6587\u4ef6\u6765\u4e3e\u4e2a\u4f8b\u5b50\uff1a<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>> gse <- getGEO(filename=system.file(\"extdata\/GSE781_family.soft.gz\"<\/span>,package=\"GEOquery\"<\/span>))<\/span><\/code><code>#\u67e5\u770b\u5143\u6570\u636e<\/span><\/span><\/code><code>> head(Meta(gse))$contact_address<\/span><\/code><code>[1<\/span>] \"715 Albany Street, E613B\"<\/span><\/span><\/code><code>$contact_city<\/span><\/code><code>[1<\/span>] \"Boston\"<\/span><\/span><\/code><code>$contact_country<\/span><\/code><code>[1<\/span>] \"USA\"<\/span><\/span><\/code><code>$contact_department<\/span><\/code><code>[1<\/span>] \"Genetics and Genomics\"<\/span><\/span><\/code><code>$contact_email<\/span><\/code><code>[1<\/span>] \"mlenburg@bu.edu\"<\/span><\/span><\/code><code>$contact_fax<\/span><\/code><code>[1<\/span>]\"617-414-1646\"<\/span><\/span><\/code><code> <\/span><\/code><code>#\u83b7\u53d6 GSE \u4e2d\u5305\u542b\u7684\u6240\u6709 GSM \u5bf9\u8c61\u7684\u540d\u79f0<\/span><\/span><\/code><code>> names<\/span>(GSMList(gse)) [1<\/span>] \"GSM11805\"<\/span> \"GSM11810\"<\/span> \"GSM11814\"<\/span> \"GSM11815\"<\/span> \"GSM11823\"<\/span> \"GSM11827\"<\/span> \"GSM11830\"<\/span> \"GSM11832\"<\/span><\/span><\/code><code> [9<\/span>] \"GSM12067\"<\/span> \"GSM12069\"<\/span> \"GSM12075\"<\/span> \"GSM12078\"<\/span> \"GSM12079\"<\/span> \"GSM12083\"<\/span> \"GSM12098\"<\/span> \"GSM12099\"<\/span><\/span><\/code><code>[17<\/span>] \"GSM12100\"<\/span> \"GSM12101\"<\/span> \"GSM12105\"<\/span> \"GSM12106\"<\/span> \"GSM12268\"<\/span> \"GSM12269\"<\/span> \"GSM12270\"<\/span> \"GSM12274\"<\/span><\/span><\/code><code>[25<\/span>] \"GSM12283\"<\/span> \"GSM12287\"<\/span> \"GSM12298\"<\/span> \"GSM12299\"<\/span> \"GSM12300\"<\/span> \"GSM12301\"<\/span> \"GSM12399\"<\/span> \"GSM12412\"<\/span><\/span><\/code><code>[33<\/span>] \"GSM12444\"<\/span> \"GSM12448\"<\/span><\/span><\/code><code> <\/span><\/code><code>#\u83b7\u5f97\u5217\u8868\u4e2d\u7684\u7b2c\u4e00\u4e2a GSM \u5bf9\u8c61<\/span><\/span><\/code><code>> GSMList(gse)[[1<\/span>]]An object of class<\/span> \"GSM\"<\/span><\/span><\/code><code>channel_count <\/span><\/code><code>[1<\/span>] \"1\"<\/span><\/span><\/code><code>comment <\/span><\/code><code>[1<\/span>] \"Raw data provided as supplementary file\"<\/span><\/span><\/code><code>contact_address <\/span><\/code><code>[1<\/span>] \"715 Albany Street, E613B\"<\/span><\/span><\/code><code>contact_city <\/span><\/code><code>[1<\/span>] \"Boston\"<\/span><\/span><\/code><code>contact_country <\/span><\/code><code>[1<\/span>] \"USA\"<\/span><\/span><\/code><code>contact_department <\/span><\/code><code>[1<\/span>] \"Genetics and Genomics\"<\/span><\/span><\/code><code>contact_email <\/span><\/code><code>[1<\/span>] \"mlenburg@bu.edu\"<\/span><\/span><\/code><code>contact_fax <\/span><\/code><code>[1<\/span>] \"617-414-1646\"<\/span><\/span><\/code><code>contact_institute <\/span><\/code><code>[1<\/span>] \"Boston University School of Medicine\"<\/span><\/span><\/code><code>contact_name <\/span><\/code><code>[1<\/span>] \"Marc,E.,Lenburg\"<\/span><\/span><\/code><code>contact_phone <\/span><\/code><code>[1<\/span>] \"617-414-1375\"<\/span><\/span><\/code><code>contact_state <\/span><\/code><code>[1<\/span>] \"MA\"<\/span><\/span><\/code><code>contact_web_link <\/span><\/code><code>[1<\/span>] \"http:\/\/gg.bu.edu\"<\/span><\/span><\/code><code>contact_zip\/postal_code <\/span><\/code><code>[1<\/span>] \"02130\"<\/span><\/span><\/code><code>data_row_count <\/span><\/code><code>[1<\/span>] \"22283\"<\/span><\/span><\/code><code>description <\/span><\/code><code>[1<\/span>] \"Age = 70; Gender = Female; Right Kidney; Adjacent Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 3; Adjacent Tumor Capsule Penetration = true; Adjacent Tumor Perinephric Fat Invasion = true; Adjacent Tumor Renal Sinus Invasion = false; Adjacent Tumor Renal Vein Invasion = true; Scaling Target = 500; Scaling Factor = 7.09; Raw Q = 2.39; Noise = 2.60; Background = 55.24.\"<\/span><\/span><\/code><code>[2<\/span>] \"Keywords = kidney\"<\/span> [3<\/span>] \"Keywords = renal\"<\/span> <\/span><\/code><code>[4<\/span>] \"Keywords = RCC\"<\/span> <\/span><\/code><code>[5<\/span>] \"Keywords = carcinoma\"<\/span> <\/span><\/code><code>[6<\/span>] \"Keywords = cancer\"<\/span> [7<\/span>] \"Lot batch = 2004638\"<\/span> <\/span><\/code><code>geo_accession <\/span><\/code><code>[1<\/span>] \"GSM11805\"<\/span><\/span><\/code><code>last_update_date <\/span><\/code><code>[1<\/span>] \"May 28 2005\"<\/span><\/span><\/code><code>molecule_ch1 <\/span><\/code><code>[1<\/span>] \"total RNA\"<\/span><\/span><\/code><code>organism_ch1 <\/span><\/code><code>[1<\/span>] \"Homo sapiens\"<\/span><\/span><\/code><code>platform_id <\/span><\/code><code>[1<\/span>] \"GPL96\"<\/span><\/span><\/code><code>series_id <\/span><\/code><code>[1<\/span>] \"GSE781\"<\/span><\/span><\/code><code>source_name_ch1 <\/span><\/code><code>[1<\/span>] \"Trizol isolation of total RNA from normal tissue adjacent to Renal Cell Carcinoma\"<\/span><\/span><\/code><code>status <\/span><\/code><code>[1<\/span>] \"Public on Nov 25 2003\"<\/span><\/span><\/code><code>submission_date <\/span><\/code><code>[1<\/span>] \"Oct 20 2003\"<\/span><\/span><\/code><code>supplementary_file <\/span><\/code><code>[1<\/span>] \"ftp:\/\/ftp.ncbi.nih.gov\/pub\/geo\/DATA\/supplementary\/samples\/GSM11nnn\/GSM11805\/GSM11805.CEL.gz\"<\/span><\/span><\/code><code>title <\/span><\/code><code>[1<\/span>] \"N035 Normal Human Kidney U133A\"<\/span><\/span><\/code><code>type <\/span><\/code><code>[1<\/span>] \"RNA\"<\/span><\/span><\/code><code>An object of class<\/span> \"GEODataTable\"<\/span><\/span><\/code><code>****** Column Descriptions ******<\/span><\/code><code> Column Description<\/span><\/code><code>1<\/span> ID_REF =<\/span><\/code><code>2<\/span> VALUE MAS 5.0<\/span> Statistical Algorithm (mean scaled to 500<\/span>)<\/span><\/code><code>3<\/span> ABS_CALL MAS 5.0<\/span> Absent, Marginal, Present call<\/span> with Alpha1 = 0.05<\/span>, Alpha2 = 0.065<\/span><\/span><\/code><code>****** Data Table ******<\/span><\/code><code> ID_REF VALUE ABS_CALL<\/span><\/code><code>1<\/span> AFFX-BioB-5<\/span>_at 953.9<\/span> P<\/span><\/code><code>2<\/span> AFFX-BioB-M_at 2982.8<\/span> P<\/span><\/code><code>3<\/span> AFFX-BioB-3<\/span>_at 1657.9<\/span> P<\/span><\/code><code>4<\/span> AFFX-BioC-5<\/span>_at 2652.7<\/span> P<\/span><\/code><code>5<\/span> AFFX-BioC-3<\/span>_at 2019.5<\/span> P<\/span><\/code><code>22278<\/span> more rows ...<\/span><\/code><\/pre>\n<\/section>\n\u600e\u4e48\u6837\uff0c\u7ecf\u8fc7\u5c0f\u5e08\u59b9\u7684\u4ecb\u7ecd\u662f\u4e0d\u662f\u5bf9GEO\u6570\u636e\u5e93\u548c\u5982\u4f55\u83b7\u53d6\u5176\u4e2d\u7684\u6570\u636e\u6709\u4e86\u66f4\u6df1\u5c42\u6b21\u7684\u4e86\u89e3\u5462\uff0c\u5982\u679c\u8fd8\u60f3\u7ee7\u7eed\u6df1\u5165\u7684\u4e86\u89e3\uff0c\u8bf7\u7ee7\u7eed\u5173\u6ce8\u5c0f\u5e08\u59b9\u7684\u6587\u7ae0\u54e6\uff0c\u90a3\u5c0f\u5e08\u59b9\u4eca\u5929\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\u5566\uff0c\u5c0f\u4f19\u4f34\u4eec\u518d\u4f1a\u3002<\/p>\n<section style=\"letter-spacing: 0.578px;caret-color: rgba(0, 0, 0, 0);text-wrap: wrap;font-size: 16px;\">\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;text-align: center;justify-content: center;display: flex;flex-flow: row nowrap;\">\n<section style=\"margin-right: 10px;display: inline-block;vertical-align: middle;width: auto;flex: 100 100 0%;height: auto;align-self: center;\">\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;\">\n<section style=\"background-color: rgb(249, 172, 172);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<section style=\"margin-right: 10px;padding-right: 8px;padding-left: 8px;display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;border-style: solid;border-width: 1px;border-color: rgb(249, 172, 172);\">\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;color: rgb(249, 172, 172);\">\nE<\/p>\n<\/section>\n<\/section>\n<section style=\"margin-right: 10px;padding-right: 8px;padding-left: 8px;display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;border-style: solid;border-width: 1px;border-color: rgb(249, 172, 172);\">\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;color: rgb(249, 172, 172);\">\nN<\/p>\n<\/section>\n<\/section>\n<section style=\"margin-right: 10px;padding-right: 8px;padding-left: 8px;display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;border-style: solid;border-width: 1px;border-color: rgb(249, 172, 172);\">\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;color: rgb(249, 172, 172);\">\nD<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 100 100 0%;height: auto;\">\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;\">\n<section style=\"background-color: rgb(249, 172, 172);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.5555555555555556\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_icWAmgGMVEzREAJmM59ov44ziaMCGg-4.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/oCSOtP61aEWjRWAeR9wicY9JyrK13cNBaR2PPYHOsBTrS4rJOUOnJCEIxt1icWAmgGMVEzREAJmM59ov44ziaMCGg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"900\" data-recalc-dims=\"1\" \/><\/p>\n<\/section>\n<mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<\/content>\n<\/div>\n<\/body> \n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"\u4e00\u5b66\u5c31\u4f1a\u5e08\u59b9\u6559\u4f60\u5982\u4f55\u7528\u00a0R\u00a0\u6765\u4e0b\u8f7d\u00a0GEO\u00a0\u7684\u6570\u636e \u5c0f\u5e08\u59b9 \u751f\u4fe1\u679c &nbsp […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/50074"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=50074"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/50074\/revisions"}],"predecessor-version":[{"id":50077,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/50074\/revisions\/50077"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=50074"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=50074"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=50074"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}