--- title: oligo：GEO/ArrayExpress芯片数据处理 tags: [] id: '1939' categories: - - uncategorized date: 2022-07-29 10:15:10 --- ## conda配置环境 * conda clean -y -all * conda create -n geo -c conda-forge r-base=4.1.3 * conda activate geo * conda install -c conda-forge r-tidyverse=1.3.1 -y * conda install -c conda-forge r-irkernel -y * conda install -c conda-forge r-r.utils -y * conda install -c conda-forge r-rcolorbrewer -y * Rscript -e "IRkernel::installspec(name='geo', displayname='r-geo')" * conda install -c bioconda bioconductor-geoquery -y * conda install -c bioconda bioconductor-oligo -y * conda install -c bioconda bioconductor-affy -y * conda install -c bioconda bioconductor-pd.hugene.1.0.st.v1 -y # read.celfiles 需要啥[安装啥](https://anaconda.org/bioconda/bioconductor-pd.hg.u133a.2) * conda install -c bioconda bioconductor-pd.hg.u133a.2 -y * conda install -c bioconda bioconductor-arrayexpress -y * conda install -c bioconda bioconductor-biomart -y * conda install -c bioconda bioconductor-affycoretools -y ## 下载芯片数据 ### GEO ```R library(GEOquery) library(oligo) library(affy) gse="GSE43332" rawdata <- getGEOSuppFiles(gse) #下载原始数据 rawdata setwd(gse) untar("GSE43332_RAW.tar",exdir = ".") celfiles <- list.files(pattern = "*CEL.gz$") #批量查找并列出后缀为.gz的文件 data.raw <- read.celfiles(celfiles) ``` ### ArrayExpress * ~/dev/xray/xray -c ~/etc/xui2.json & * wget -e "https\_proxy=http://127.0.0.1:20809" https://www.ebi.ac.uk/arrayexpress/files/E-MEXP-1422/E-MEXP-1422.raw.1.zip -O E-MEXP-1422.raw.1.zip * unzip E-MEXP-1422.raw.1.zip ```R library(ArrayExpress) library(oligo) library(affy) # Sys.setenv("http_proxy"="http://127.0.0.1:20809") # Sys.setenv("https_proxy"="http://127.0.0.1:20809") # mexp1422=getAE("E-MTAB-6128", type = 'raw', extract = T) celfiles <- list.files(pattern = "*.CEL$") #批量查找并列出后缀为CEL的文件 data.raw <- read.celfiles(celfiles) ``` ## RMA标准化数据 ```R sampleNames(data.raw) <- sapply(strsplit(sampleNames(data.raw),"_",fixed=T), "[",1) sampleNames(data.raw) fit1 <- fitProbeLevelModel(data.raw) image(fit1,type="weights",which=1,main="weights") image(fit1,type="residuals",which=1,main="Residuals") image(fit1,type="sign.residuals",which=1,main="Residuals.sign") data.eset <- oligo::rma(data.raw) data.exprs <- exprs(data.eset) library(RColorBrewer) display.brewer.all() if(ncol(data.eset)>8){ colors <- c(brewer.pal(8,"Set2"),brewer.pal(ncol(data.eset)-8,"Set1")) }else{ colors <- brewer.pal(ncol(data.eset),"Set2") } boxplot(data.exprs,col=colors,main="afterRMA") ``` ## 探针转Symbol * [f\_dedup\_IQR 函数来源](https://occdn.limour.top/2157.html) * data.raw@annotation 可以得到注释的包信息，如pd.hg.u133a.2 * 在[bioconductor](https://www.bioconductor.org/)上搜索pd.hg.u133a.2，可以知道其Platform为HG-U133A\_2 * 谷歌搜索 HG-U133A\_2 + affymetrix，可以找到affymetrix官网对应的页面 * 谷歌搜索 affymetrix "HG-U133A\_2" site:www.ncbi.nlm.nih.gov，随便进一个GSE页面，找到对应的Platforms，如 GPL571 \[HG-U133A\_2\] Affymetrix Human Genome U133A 2.0 Array，说明HG-U133A\_2对应GPL571 ```R require(GEOquery) f_getGPL <- function(lc_GPLN, lc_local = F){ options(stringsAsFactors = F) if (!file.exists(lc_GPLN)){dir.create(lc_GPLN)} if(lc_local){ gpl=read.table(file.path(lc_GPLN, lc_GPLN), header = TRUE,fill = T,sep = "\t", comment.char = "#", stringsAsFactors = FALSE, quote = "") return(gpl) }else{ return(Table(getGEO(lc_GPLN,destdir = lc_GPLN))) } } GPL <- 'GPL6244' GPL <- f_getGPL(GPL) GPL[['Symbol']] <- GPL$gene_assignment GPL <- GPL[c('ID','Symbol')] GPL[GPL$Symbol == '---', 'Symbol'] = '---//---' tmp <- strsplit(x = GPL$Symbol, split = '//') tmp <- lapply(tmp, FUN = function(x){x[2]}) GPL[['Symbol']] = unlist(tmp) GPL$Symbol[GPL$Symbol == '---'] = GPL$ID[GPL$Symbol == '---'] rownames(GPL) <- as.character(GPL$ID) GPL <- GPL[as.character(rownames(data.exprs)),] data.exprs <- f_dedup_IQR(data.exprs, GPL$Symbol) data.exprs ``` ## GPL与Platform对应表 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 \[CDF: Brainarray HuGene11stv1\_Hs\_ENTREZG\_15.1.0\] 来自：[爱代码爱编程](https://icode.best/i/32522930456304)