{"id":65544,"date":"2026-10-07T17:00:00","date_gmt":"2026-10-07T09:00:00","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=65544"},"modified":"2026-10-06T13:35:25","modified_gmt":"2026-10-06T05:35:25","slug":"reviewer-batch-effect","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/reviewer-batch-effect\/","title":{"rendered":"\u5ba1\u7a3f\u4eba\u8bf4\u6709\u6279\u6b21\u6548\u5e94\uff1a\u8981\u91cd\u8dd1\u5168\u90e8\u5206\u6790\uff0c\u8fd8\u662f\u5148\u8865\u4e00\u5f20\u8868\uff1f"},"content":{"rendered":"<p>PCA \u56fe\u88ab\u5ba1\u7a3f\u4eba\u5708\u51fa\u6765\uff1a\u201cThe observed separation may be driven by batch effects.\u201d \u8fd9\u65f6\u6700\u5bb9\u6613\u53d1\u751f\u7684\u8fd4\u5de5\uff0c\u662f\u76f4\u63a5\u6362\u4e00\u79cd\u53bb\u6279\u6b21\u65b9\u6cd5\uff0c\u76f4\u5230\u4e24\u56e2\u70b9\u6df7\u5728\u4e00\u8d77\u3002\u56fe\u53ef\u80fd\u66f4\u597d\u770b\u4e86\uff0c\u95ee\u9898\u5374\u672a\u5fc5\u89e3\u51b3\u3002<\/p>\n<p>\u5148\u628a\u6837\u672c\u6e05\u5355\u627e\u9f50\uff1a\u6837\u672c\u7f16\u53f7\u3001\u5b9e\u9a8c\u5206\u7ec4\u3001\u91c7\u6837\u65f6\u95f4\u3001\u5efa\u5e93\u6279\u6b21\u3001\u6d4b\u5e8f\u6279\u6b21\uff0c\u4ee5\u53ca\u540c\u4e00\u4eba\u7684\u914d\u5bf9\u5173\u7cfb\u3002\u7528\u5206\u7ec4\u548c\u6279\u6b21\u505a\u4e00\u4e2a\u4ea4\u53c9\u8868\u3002\u5982\u679c\u6240\u6709\u75c5\u4f8b\u90fd\u5728\u7b2c\u4e00\u6279\uff0c\u6240\u6709\u5bf9\u7167\u90fd\u5728\u7b2c\u4e8c\u6279\uff0c\u8f6f\u4ef6\u6ca1\u6709\u8db3\u591f\u7684\u4fe1\u606f\u5206\u5f00\u201c\u75be\u75c5\u6548\u5e94\u201d\u548c\u201c\u6279\u6b21\u6548\u5e94\u201d\u3002<\/p>\n<figure style=\"margin:28px 0\"><a href=\"https:\/\/www.biocloudservice.com\/revision-assistant\/assets\/diagrams\/batch-effect.svg\" target=\"_blank\" rel=\"noopener\"><img decoding=\"async\" src=\"https:\/\/www.biocloudservice.com\/revision-assistant\/assets\/diagrams\/batch-effect.svg\" alt=\"\u6279\u6b21\u6548\u5e94\u8fd4\u4fee\uff1a\u56db\u4e2a\u68c0\u67e5\u70b9\uff1a\u5217\u51fa\u6837\u672c\u4fe1\u606f\uff0c\u5206\u7ec4 \u00d7 \u6279\u6b21 \u00d7 \u914d\u5bf9\uff1b\u68c0\u67e5\u53ef\u8bc6\u522b\u6027\uff0c\u5b8c\u5168\u6df7\u6742\u4e0d\u80fd\u786c\u6821\u6b63\uff1b\u533a\u5206\u4f5c\u56fe\u4e0e\u68c0\u9a8c\uff0c\u5d4c\u5165\u6df7\u5408\u4e0d\u7b49\u4e8e\u53ef\u76f4\u63a5\u68c0\u9a8c\uff1b\u8ffd\u8e2a\u4e0b\u6e38\u53d8\u5316\uff0c\u5dee\u5f02\u3001\u5bcc\u96c6\u3001\u6b63\u6587\u540c\u6b65\u6539\" width=\"960\" height=\"610\" loading=\"lazy\" style=\"width:100%;height:auto;border-radius:16px\"><\/a><figcaption style=\"font-size:13px;color:#637982\">\u6279\u6b21\u6548\u5e94\u8fd4\u4fee\uff1a\u56db\u4e2a\u68c0\u67e5\u70b9\u3002\u65b9\u6cd5\u793a\u610f\uff0c\u4e0d\u662f\u5b9e\u9a8c\u7ed3\u679c\u3002\u70b9\u51fb\u53ef\u653e\u5927\u3002<\/figcaption><\/figure>\n<h2 id=\"section-2\">\u8fd9\u4e09\u79cd\u60c5\u51b5\uff0c\u5904\u7406\u65b9\u5f0f\u4e0d\u540c<\/h2>\n<div class=\"revision-table\" style=\"margin:24px 0\" role=\"region\" aria-label=\"\u5148\u770b\u8bbe\u8ba1\uff0c\u518d\u51b3\u5b9a\u662f\u5426\u91cd\u7b97\uff08\u60c5\u5f62\u793a\u610f\uff09\" tabindex=\"0\">\n<table style=\"width:100%;min-width:570px;border-collapse:collapse;font-size:14px;line-height:1.8\">\n<caption style=\"text-align:left;padding:0 0 12px;font-weight:600\">\u5148\u770b\u8bbe\u8ba1\uff0c\u518d\u51b3\u5b9a\u662f\u5426\u91cd\u7b97\uff08\u60c5\u5f62\u793a\u610f\uff09<\/caption>\n<thead>\n<tr>\n<th scope=\"col\" style=\"padding:14px;text-align:left;background:#173d4a;color:white;border:1px solid #d6e3e2\">\u6837\u672c\u8bbe\u8ba1<\/th>\n<th scope=\"col\" style=\"padding:14px;text-align:left;background:#173d4a;color:white;border:1px solid #d6e3e2\">\u4f18\u5148\u5904\u7406<\/th>\n<th scope=\"col\" style=\"padding:14px;text-align:left;background:#173d4a;color:white;border:1px solid #d6e3e2\">\u4e0d\u8981\u8fd9\u6837\u505a<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"padding:14px;border:1px solid #d6e3e2;vertical-align:top\">\u6bcf\u4e2a\u6279\u6b21\u90fd\u6709\u75c5\u4f8b\u4e0e\u5bf9\u7167<\/td>\n<td style=\"padding:14px;border:1px solid #d6e3e2;vertical-align:top\">\u6838\u5bf9\u8d28\u91cf\u540e\uff0c\u5728\u5408\u9002\u7684\u7edf\u8ba1\u8bbe\u8ba1\u4e2d\u7eb3\u5165\u6279\u6b21<\/td>\n<td style=\"padding:14px;border:1px solid #d6e3e2;vertical-align:top\">\u53ea\u5728\u65b9\u6cd5\u91cc\u8865\u5199\u201c\u53bb\u6279\u6b21\u201d<\/td>\n<\/tr>\n<tr>\n<td style=\"padding:14px;border:1px solid #d6e3e2;vertical-align:top\">\u5404\u6279\u6b21\u6709\u90e8\u5206\u91cd\u53e0\uff0c\u4f46\u5206\u5e03\u4e0d\u5747<\/td>\n<td style=\"padding:14px;border:1px solid #d6e3e2;vertical-align:top\">\u68c0\u67e5\u8bbe\u8ba1\u77e9\u9635\u4e0e\u4f30\u8ba1\u7a33\u5b9a\u6027\uff0c\u8bf4\u660e\u4e0d\u5e73\u8861<\/td>\n<td style=\"padding:14px;border:1px solid #d6e3e2;vertical-align:top\">\u9ed8\u8ba4\u52a0\u4e0a batch \u5c31\u4e07\u4e8b\u5927\u5409<\/td>\n<\/tr>\n<tr>\n<td style=\"padding:14px;border:1px solid #d6e3e2;vertical-align:top\">\u6279\u6b21\u4e0e\u5b9e\u9a8c\u5206\u7ec4\u5b8c\u5168\u91cd\u5408<\/td>\n<td style=\"padding:14px;border:1px solid #d6e3e2;vertical-align:top\">\u5bfb\u6c42\u53ef\u6bd4\u8865\u5145\u6837\u672c\uff0c\u6216\u6536\u7f29\u53ef\u56de\u7b54\u7684\u95ee\u9898<\/td>\n<td style=\"padding:14px;border:1px solid #d6e3e2;vertical-align:top\">\u5220\u9664\u5206\u7ec4\u4fe1\u606f\u6765\u8ba9\u6a21\u578b\u6210\u529f\u8fd0\u884c<\/td>\n<\/tr>\n<tr>\n<td style=\"padding:14px;border:1px solid #d6e3e2;vertical-align:top\">\u5355\u7ec6\u80de\u6574\u5408\u540e\u505a\u5dee\u5f02\u68c0\u9a8c<\/td>\n<td style=\"padding:14px;border:1px solid #d6e3e2;vertical-align:top\">\u6838\u5bf9\u7528\u4e8e\u68c0\u9a8c\u7684\u6570\u636e\u5c42\u53ca\u6837\u672c\u5c42\u7ea7\u8bbe\u8ba1<\/td>\n<td style=\"padding:14px;border:1px solid #d6e3e2;vertical-align:top\">\u628a UMAP \u6df7\u5408\u89c6\u4e3a\u5dee\u5f02\u5206\u6790\u5df2\u65e0\u504f<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n<p>DESeq2 \u6587\u6863\u89e3\u91ca\u4e86\u8bbe\u8ba1\u77e9\u9635\u4e0d\u6ee1\u79e9\u7684\u95ee\u9898\u3002\u5bf9\u9002\u7528\u7684 bulk RNA-seq \u8ba1\u6570\u6a21\u578b\uff0c\u6279\u6b21\u53ef\u4ee5\u4f5c\u4e3a\u8bbe\u8ba1\u4e2d\u7684\u4e00\u4e2a\u56e0\u7d20\uff1b\u4f46\u524d\u63d0\u662f\u8bbe\u8ba1\u5141\u8bb8\u4f30\u8ba1\u76f8\u5e94\u6548\u5e94\u3002\u4e0d\u80fd\u628a\u201c\u6a21\u578b\u62a5\u9519\u201d\u7406\u89e3\u6210\u53ea\u9700\u968f\u610f\u5220\u9664\u4e00\u4e2a\u53d8\u91cf\u3002<\/p>\n<h2 id=\"section-5\">\u54ea\u4e9b\u4e1c\u897f\u5fc5\u987b\u91cd\u8dd1\uff0c\u54ea\u4e9b\u4e0d\u7528<\/h2>\n<p>\u5148\u753b\u4f9d\u8d56\u5173\u7cfb\uff1a\u5dee\u5f02\u5206\u6790 \u2192 \u5bcc\u96c6 \u2192 \u5019\u9009\u57fa\u56e0\u7b5b\u9009 \u2192 \u6b63\u6587\u7ed3\u8bba\u3002\u5982\u679c\u7edf\u8ba1\u6a21\u578b\u53d8\u4e86\uff0c\u8fd9\u6761\u94fe\u4e0a\u7684\u8f93\u51fa\u90fd\u8981\u6838\u5bf9\u3002\u5e76\u4e0d\u610f\u5473\u7740\u4ece FASTQ \u5f00\u59cb\u5168\u90e8\u91cd\u505a\uff1b\u6bd4\u5bf9\u548c\u8ba1\u6570\u6ca1\u6709\u95ee\u9898\u65f6\uff0c\u53ef\u4ece\u53d7\u5f71\u54cd\u7684\u7edf\u8ba1\u6b65\u9aa4\u91cd\u7b97\u3002\u76f8\u53cd\uff0c\u53ea\u6539 PCA \u56fe\u800c\u4fdd\u7559\u65e7\u7684\u5dee\u5f02\u7ed3\u679c\uff0c\u4e5f\u4e0d\u7b97\u5b8c\u6210\u4fee\u8ba2\u3002<\/p>\n<p>\u4f5c\u56fe\u6570\u636e\u548c\u68c0\u9a8c\u6570\u636e\u8981\u5206\u5f00\u8bf4\u660e\u3002\u7528\u4e8e\u53ef\u89c6\u5316\u7684\u8f6c\u6362\u6216\u6574\u5408\u7ed3\u679c\uff0c\u4e0d\u5e94\u4e0d\u52a0\u5224\u65ad\u5730\u5582\u7ed9\u539f\u672c\u9488\u5bf9\u539f\u59cb\u8ba1\u6570\u8bbe\u8ba1\u7684\u68c0\u9a8c\u3002\u5355\u7ec6\u80de\u9879\u76ee\u8fd8\u8981\u5199\u6e05\u6574\u5408\u65b9\u6cd5\u3001\u4f7f\u7528\u7684\u6570\u636e\u5c42\uff0c\u4ee5\u53ca\u5dee\u5f02\u5206\u6790\u662f\u5426\u4fdd\u7559\u4e86\u751f\u7269\u5b66\u91cd\u590d\u7684\u4fe1\u606f\u3002Seurat \u7684\u6574\u5408\u6559\u7a0b\u53ef\u7528\u4e8e\u6838\u5bf9\u5b9e\u73b0\u7ec6\u8282\uff0c\u4e0d\u80fd\u636e\u6b64\u4fdd\u8bc1\u6240\u6709\u4e0b\u6e38\u68c0\u9a8c\u90fd\u6709\u6548\u3002<\/p>\n<h2 id=\"section-8\">\u56de\u590d\u4fe1\u91cc\u5e94\u5f53\u51fa\u73b0\u54ea\u4e9b\u8bc1\u636e<\/h2>\n<ul>\n<li>\u4e00\u5f20\u5206\u7ec4 \u00d7 \u6279\u6b21\u6837\u672c\u5206\u5e03\u8868\uff0c\u8ba9\u4eba\u770b\u6e05\u8bbe\u8ba1\u3002<\/li>\n<li>\u6821\u6b63\u6216\u8c03\u6574\u524d\u540e\u7684\u8bca\u65ad\u56fe\uff0c\u4f7f\u7528\u53ef\u6bd4\u8f83\u7684\u6807\u6ce8\u4e0e\u5c3a\u5ea6\u3002<\/li>\n<li>\u5b9e\u9645\u7edf\u8ba1\u8bbe\u8ba1\u4e0e\u5bf9\u6bd4\u65b9\u5411\uff0c\u4ee5\u53ca\u6838\u5fc3\u7ed3\u679c\u662f\u5426\u6539\u53d8\u3002<\/li>\n<li>\u66f4\u65b0\u540e\u7684\u56fe\u8868\u7f16\u53f7\uff1b\u82e5\u7ed3\u8bba\u53d8\u5316\uff0c\u660e\u786e\u5199\u53d8\u5316\uff0c\u4e0d\u56de\u907f\u3002<\/li>\n<\/ul>\n<blockquote style=\"border-left:3px solid #008078;background:#f0f7f6;padding:20px 24px\">\n<p lang=\"en\">We examined the distribution of samples across [batch variable] and [study group] (Table [X]). We then [actually completed adjustment or sensitivity analysis], using [model\/design]. The revised results are shown in [location]. Compared with the original analysis, [describe the actual changes]. We have updated [affected figures and conclusions] accordingly.<\/p>\n<\/blockquote>\n<p style=\"font-size:13px;color:#61747c\">\u8fd9\u662f\u53ef\u4fee\u6539\u7684\u5199\u4f5c\u6846\u67b6\uff0c\u4e0d\u662f\u5bf9\u4f60\u7684\u7814\u7a76\u7ed3\u679c\u7684\u9648\u8ff0\uff1b\u672a\u5b8c\u6210\u7684\u5de5\u4f5c\u4e0d\u5f97\u5199\u6210\u5df2\u5b8c\u6210\u3002<\/p>\n<p>\u5982\u679c\u5b8c\u5168\u6df7\u6742\uff0c\u5c31\u628a\u6a21\u677f\u91cc\u7684\u5206\u6790\u6b65\u9aa4\u6362\u6210\u4e8b\u5b9e\uff1a\u54ea\u4e9b\u6548\u5e94\u65e0\u6cd5\u533a\u5206\u3001\u8fd8\u9700\u8981\u4ec0\u4e48\u6570\u636e\u3001\u6587\u7ae0\u56e0\u6b64\u5220\u51cf\u4e86\u4ec0\u4e48\u5224\u65ad\u3002\u4e0d\u8981\u5199\u201c\u6279\u6b21\u6548\u5e94\u5df2\u5b8c\u5168\u6d88\u9664\u201d\u2014\u2014\u8fd9\u53e5\u8bdd\u6bd4\u5c55\u793a\u4e00\u5f20\u6df7\u5408\u826f\u597d\u7684\u56fe\u9700\u8981\u5f3a\u5f97\u591a\u7684\u8bc1\u636e\u3002<\/p>\n<aside style=\"background:#edf7f4;border:1px solid #c7e0da;border-radius:14px;padding:24px;margin:34px 0\">\n<h2 style=\"margin-top:0\">\u628a\u4f60\u624b\u4e0a\u7684\u90a3\u6761\u610f\u89c1\uff0c\u6574\u7406\u6210\u5de5\u4f5c\u5355<\/h2>\n<p>\u5982\u679c\u8fd8\u62ff\u4e0d\u51c6\u4ece\u54ea\u91cc\u5f00\u59cb\uff0c\u53ef\u4ee5\u4f7f\u7528\u4e91\u751f\u4fe1\u7684<a href=\"https:\/\/www.biocloudservice.com\/revision-assistant\/?topic=batch&amp;from=batch-effect\">\u5ba1\u7a3f\u610f\u89c1\u8fd4\u4fee\u52a9\u624b<\/a>\u3002\u4e0d\u7528\u767b\u5f55\u6216\u7559\u7535\u8bdd\uff0c\u5148\u5f97\u5230\u5904\u7406\u8def\u5f84\u3001\u6750\u6599\u6e05\u5355\u548c\u53ef\u7f16\u8f91\u7684\u56de\u590d\u6846\u67b6\uff0c\u590d\u5236\u548c\u4e0b\u8f7d\u4e5f\u514d\u8d39\u3002<\/p>\n<p>\u9700\u8981\u4eba\u4e00\u8d77\u5224\u65ad\u65f6\uff0c\u518d\u81ea\u613f\u7533\u8bf7\u6280\u672f\u4eba\u5458\u590d\u6838\u3002\u6d89\u53ca\u5206\u6790\u670d\u52a1\u7684\u8303\u56f4\u4e0e\u8d39\u7528\uff0c\u53e6\u884c\u6c9f\u901a\u786e\u8ba4\uff0c\u4e0d\u627f\u8bfa\u5f55\u7528\u7ed3\u679c\u3002<\/p>\n<p><a href=\"https:\/\/www.biocloudservice.com\/revision-assistant\/?topic=batch&amp;from=batch-effect\" style=\"display:inline-block;background:#007d7b;color:white;padding:11px 20px;border-radius:8px;text-decoration:none\">\u5148\u68b3\u7406\u8fd9\u4e00\u6761\u5ba1\u7a3f\u610f\u89c1 \u2192<\/a><\/p>\n<\/aside>\n<h2>\u53c2\u8003\u4e0e\u66f4\u65b0<\/h2>\n<p>\u672c\u6587\u7684\u5904\u7406\u6b65\u9aa4\u4e3a\u7f16\u8f91\u6574\u7406\u7684\u5b9e\u8df5\u5efa\u8bae\uff0c\u9700\u7ed3\u5408\u7814\u7a76\u8bbe\u8ba1\u5224\u65ad\uff1b\u793a\u4f8b\u4e0d\u662f\u5ba2\u6237\u6848\u4f8b\uff0c\u8868\u683c\u4e0d\u5305\u542b\u865a\u6784\u5b9e\u6d4b\u6570\u636e\u3002<\/p>\n<ul>\n<li><a href=\"https:\/\/bioconductor.org\/packages\/release\/bioc\/vignettes\/DESeq2\/inst\/doc\/DESeq2.html#model-matrix-not-full-rank\" target=\"_blank\" rel=\"noopener noreferrer\">DESeq2\uff1a\u8bbe\u8ba1\u77e9\u9635\u4e0d\u6ee1\u79e9\u4e0e\u591a\u56e0\u7d20\u8bbe\u8ba1<\/a><\/li>\n<li><a href=\"https:\/\/satijalab.org\/seurat\/articles\/integration_introduction\" target=\"_blank\" rel=\"noopener noreferrer\">Seurat\uff1a\u5355\u7ec6\u80de\u6574\u5408\u6559\u7a0b<\/a><\/li>\n<\/ul>\n<p style=\"font-size:13px;color:#637982\">\u4e91\u751f\u4fe1 \u00b7 \u5ba1\u7a3f\u4e0e\u8fd4\u4fee\u7cfb\u5217 \u00b7 \u5185\u5bb9\u6838\u5bf9\u65e5\u671f 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