GEO生信数据挖掘（二）下载基因芯片平台文件及注释
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为例上节我们，但是矩阵行名称是芯片探针需要转换为基因名。
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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
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）
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_set=annotation[,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
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL96
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_set=platform_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
| GPL96 | hgu133a |
# 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]
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