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下载平台文件
1.AnnotGPL参数改为TRUE,联网下载芯片平台的soft文件。#xff08;国内网速奇慢经常中断#xff09;
2.手工去GEO官网下载
转换芯片探针ID为gene name
拓… 检索到目标数据集后开始数据挖掘本文以阿尔兹海默症数据集GSE1297为例 目录
下载平台文件
1.AnnotGPL参数改为TRUE,联网下载芯片平台的soft文件。国内网速奇慢经常中断
2.手工去GEO官网下载
转换芯片探针ID为gene name
拓展通过bioconductor注释包
# 找到GPL6244相应的注释包hgu133a.db 上节我们下载了GEO数据集并提取了基因表达矩阵但是矩阵行名称是芯片探针需要转换为基因名。 下载平台文件
1.AnnotGPL参数改为TRUE,联网下载芯片平台的soft文件。国内网速奇慢经常中断
注意下载好soft文件才可以直接可以提取注释没下载好注释内容全为空后续代码可以运行但是不能得到正确数据的矩阵。
# 提取注释信息 annotation - featureData(gse_info[[1]])
library(GEOquery)
# 指定GEO数据集的ID
gse_id - GSE1297
# 使用getGEO函数获取数据集的基础信息
gse_info - getGEO(gse_id, destdir ., AnnotGPL TRUE )# 提取注释信息
annotation - featureData(gse_info[[1]]) #下载好soft可以直接可以提取注释没下载好注释内容全为空#查看平台文件列名
colnames(annotation)#仅提取两列第一列芯片探针名第十一列基因名
platform_file_setannotation[,c(1,11)]#还可以尝试单独下载GPL96平台文件
gse_gp-getGEO(GPL96,destdir .) # 网速不佳 下载失败提示 Failed to download ./GPL96.soft.gz! 2.手工去GEO官网下载
GEO Accession viewerNCBIs Gene Expression Omnibus (GEO) is a public archive and resource for gene expression data.https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?accGPL96 dir() #打印项目文件列表
# 读取芯片平台文件txt
platform_file - read.delim(GPL96-57554.txt, header TRUE, sep \t, comment.char #)
#查看平台文件列名
colnames(platform_file)#仅提取两列第一列芯片探针名第十一列基因名
platform_file_setplatform_file[,c(1,11)] 转换芯片探针ID为gene name
先将上节中提取到的表达矩阵转换格式。
表达矩阵是Matrix对象而我们接下来要用到的merge函数不能对Matrix对象使用因此要先将表达矩阵转换为data.frame对象。否则会报错。Error in fix.by(by.x, x) : by必需指定唯一有效的列。
#将Matrix格式表达矩阵转换为data.frame格式
exprSet - data.frame(expression_data)#给表达矩阵新增加一列ID
exprSet$ID - rownames(exprSet) # 得到表达矩阵行名为ID需要转换新增一列#矩阵表达文件和平台文件有相同列‘ID’使用merge函数合并
express - merge(x exprSet, y platform_file_set, by.x ID)#删除探针ID列
express$ID NULL 最终将探针ID列删除剩余32列即得到有基因名称的表达矩阵。
大家观察最后一列一个芯片探针匹配到多个基因下节我们来看看处理方案。 拓展通过bioconductor注释包
GPL96hgu133a
# 找到GPL6244相应的注释包hgu133a.db
gpl bioc_package title GPL32 mgu74a [MG_U74A] Affymetrix Murine Genome U74A Array GPL33 mgu74b [MG_U74B] Affymetrix Murine Genome U74B Array GPL34 mgu74c [MG_U74C] Affymetrix Murine Genome U74C Array GPL71 ag [AG] Affymetrix Arabidopsis Genome Array GPL72 drosgenome1 [DrosGenome1] Affymetrix Drosophila Genome Array GPL74 hcg110 [HC_G110] Affymetrix Human Cancer Array GPL75 mu11ksuba [Mu11KsubA] Affymetrix Murine 11K SubA Array GPL76 mu11ksubb [Mu11KsubB] Affymetrix Murine 11K SubB Array GPL77 mu19ksuba [Mu19KsubA] Affymetrix Murine 19K SubA Array GPL78 mu19ksubb [Mu19KsubB] Affymetrix Murine 19K SubB Array GPL79 mu19ksubc [Mu19KsubC] Affymetrix Murine 19K SubC Array GPL80 hu6800 [Hu6800] Affymetrix Human Full Length HuGeneFL Array GPL81 mgu74av2 [MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array GPL82 mgu74bv2 [MG_U74Bv2] Affymetrix Murine Genome U74B Version 2 Array GPL83 mgu74cv2 [MG_U74Cv2] Affymetrix Murine Genome U74 Version 2 Array GPL85 rgu34a [RG_U34A] Affymetrix Rat Genome U34 Array GPL86 rgu34b [RG_U34B] Affymetrix Rat Genome U34 Array GPL87 rgu34c [RG_U34C] Affymetrix Rat Genome U34 Array GPL88 rnu34 [RN_U34] Affymetrix Rat Neurobiology U34 Array GPL89 rtu34 [RT_U34] Affymetrix Rat Toxicology U34 Array GPL90 ygs98 [YG_S98] Affymetrix Yeast Genome S98 Array GPL91 hgu95av2 [HG_U95A] Affymetrix Human Genome U95A Array GPL92 hgu95b [HG_U95B] Affymetrix Human Genome U95B Array GPL93 hgu95c [HG_U95C] Affymetrix Human Genome U95C Array GPL94 hgu95d [HG_U95D] Affymetrix Human Genome U95D Array GPL95 hgu95e [HG_U95E] Affymetrix Human Genome U95E Array GPL96 hgu133a [HG-U133A] Affymetrix Human Genome U133A Array GPL97 hgu133b [HG-U133B] Affymetrix Human Genome U133B Array GPL98 hu35ksuba [Hu35KsubA] Affymetrix Human 35K SubA Array GPL99 hu35ksubb [Hu35KsubB] Affymetrix Human 35K SubB Array GPL100 hu35ksubc [Hu35KsubC] Affymetrix Human 35K SubC Array GPL101 hu35ksubd [Hu35KsubD] Affymetrix Human 35K SubD Array GPL198 ath1121501 [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array GPL199 ecoli2 [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array GPL200 celegans [Celegans] Affymetrix C. elegans Genome Array GPL201 hgfocus [HG-Focus] Affymetrix Human HG-Focus Target Array GPL339 moe430a [MOE430A] Affymetrix Mouse Expression 430A Array GPL340 mouse4302 [MOE430B] Affymetrix Mouse Expression 430B Array GPL341 rae230a [RAE230A] Affymetrix Rat Expression 230A Array GPL342 rae230b [RAE230B] Affymetrix Rat Expression 230B Array GPL570 hgu133plus2 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array GPL571 hgu133a2 [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array GPL886 hgug4111a Agilent-011871 Human 1B Microarray G4111A (Feature Number version) GPL887 hgug4110b Agilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version) GPL1261 mouse430a2 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array GPL1318 xenopuslaevis [Xenopus_laevis] Affymetrix Xenopus laevis Genome Array GPL1319 zebrafish [Zebrafish] Affymetrix Zebrafish Genome Array GPL1322 drosophila2 [Drosophila_2] Affymetrix Drosophila Genome 2.0 Array GPL1352 u133x3p [U133_X3P] Affymetrix Human X3P Array GPL1355 rat2302 [Rat230_2] Affymetrix Rat Genome 230 2.0 Array GPL1708 hgug4112a Agilent-012391 Whole Human Genome Oligo Microarray G4112A (Feature Number version) GPL2112 bovine [Bovine] Affymetrix Bovine Genome Array GPL2529 yeast2 [Yeast_2] Affymetrix Yeast Genome 2.0 Array GPL2891 h20kcod GE Healthcare/Amersham Biosciences CodeLink™ UniSet Human 20K I Bioarray GPL2898 adme16cod GE Healthcare/Amersham Biosciences CodeLink™ ADME Rat 16-Assay Bioarray GPL3154 ecoli2 [E_coli_2] Affymetrix E. coli Genome 2.0 Array GPL3213 chicken [Chicken] Affymetrix Chicken Genome Array GPL3533 porcine [Porcine] Affymetrix Porcine Genome Array GPL3738 canine2 [Canine_2] Affymetrix Canine Genome 2.0 Array GPL3921 hthgu133a [HT_HG-U133A] Affymetrix HT Human Genome U133A Array GPL3979 canine [Canine] Affymetrix Canine Genome 1.0 Array GPL4032 [Maize] Affymetrix Maize Genome Array GPL4191 h10kcod CodeLink UniSet Human I Bioarray GPL5188 huex10sttranscriptcluster [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version] GPL5689 hgug4100a Agilent Human 1 cDNA Microarray (G4100A) [layout C] GPL6097 illuminaHumanv1 Illumina human-6 v1.0 expression beadchip GPL6102 illuminaHumanv2 Illumina human-6 v2.0 expression beadchip GPL6244 hugene10sttranscriptcluster [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] GPL6246 mogene10sttranscriptcluster [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] GPL6885 illuminaMousev2 Illumina MouseRef-8 v2.0 expression beadchip GPL6947 illuminaHumanv3 Illumina HumanHT-12 V3.0 expression beadchip GPL8300 hgu95av2 [HG_U95Av2] Affymetrix Human Genome U95 Version 2 Array GPL8321 mouse430a2 [Mouse430A_2] Affymetrix Mouse Genome 430A 2.0 Array GPL8490 IlluminaHumanMethylation27k Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2) GPL10558 illuminaHumanv4 Illumina HumanHT-12 V4.0 expression beadchip GPL11532 hugene11sttranscriptcluster [HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [transcript (gene) version] GPL13497 HsAgilentDesign026652 Agilent-026652 Whole Human Genome Microarray 4x44K v2 (Probe Name version) GPL13534 IlluminaHumanMethylation450k Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) GPL13667 hgu219 [HG-U219] Affymetrix Human Genome U219 Array GPL14877 hgu133plus2 Affymetrix Human Genome U133 Plus 2.0 Array [Brainarray Version 13, HGU133Plus2_Hs_ENTREZG] GPL15380 GGHumanMethCancerPanelv1 Illumina Sentrix Array Matrix (SAM) - GoldenGate Methylation Cancer Panel I GPL15396 hthgu133b [HT_HG-U133B] Affymetrix HT Human Genome U133B Array [custom CDF: ENTREZ brainarray v. 14] GPL17556 hugene10sttranscriptcluster [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZG_17.0.0] GPL17897 hthgu133a [HT_HG-U133A] Affymetrix Human Genome U133A Array (custom CDF: HTHGU133A_Hs_ENTREZG.cdf version 17.0.0) GPL18190 hugene11sttranscriptcluster [HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [CDF: Brainarray HuGene11stv1_Hs_ENTREZG_15.1.0]
