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2022-07-29-【迁移】oligo：GEO-ArrayExpress芯片数据处理.md

2022-07-29-【迁移】oligo：GEO-ArrayExpress芯片数据处理.md 18 KB
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title: 【迁移】oligo：GEO/ArrayExpress芯片数据处理 urlname: oligo-GEO-ArrayExpress-xin-pian-shu-ju-chu-li date: 2022-07-29 19:00:11 index_img: https://api.limour.top/randomImg?d=2022-07-29 19:00:11

tags: ['oligo', 'GEO', 'ArrayExpress']

安装依赖

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
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

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

    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

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

使用IQR方法进行重复值的选择

使用 rownames(df) <- rowNn 时经常会遇到rowNn中有重复值的情况，此时需要使用合适的策略来选择需要保留的那一列。下面这个函数默认保留IQR值(四分位距)最大的那一列。通过传入不同的select_func参数值，也可以改用其他的保留选择策略。如 mean 来保留算数平均值最大的一列，也可以传入自己定义的函数。

f_rm_duplicated <- function(NameL, reverse=F){
    tmp <- data.frame(table(NameL))
    if(reverse){
        tmp <- tmp$NameL[tmp$Freq > 1]
    }else{
        tmp <- tmp$NameL[tmp$Freq == 1]
    }
    which(NameL %in% as.character(tmp))
}
f_dedup_IQR <- function(df, rowNn, select_func='IQR'){
    if(typeof(select_func) == 'character'){
        select_func = get(select_func)
    }
    # 拆出无重复的数据，后续不进行处理
    noDup <- f_rm_duplicated(rowNn)
    tmp <- rowNn[noDup]
    noDup <- df[noDup,]
    rownames(noDup) <- tmp
    # 拆除有重复的数据
    Dup <- f_rm_duplicated(rowNn, T)
    rowNn <- rowNn[Dup]
    Dup <- df[Dup,]
    rownames(Dup) <- NULL
    # 处理重复的数据
    lc_tmp = by(Dup,
         rowNn,
         function(x){rownames(x)[which.max(apply(X = x, FUN = select_func, MARGIN = 1))]})
    lc_probes = as.integer(lc_tmp)
    Dup = Dup[lc_probes,]
    rownames(Dup) <- rowNn[lc_probes]
    # 合并数据并返回
    return(rbind(noDup,Dup))
}

探针转Symbol

  • data.raw@annotation 可以得到注释的包信息，如pd.hg.u133a.2
  • 在bioconductor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

    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]