【迁移】oligo：GEO/ArrayExpress芯片数据处理

Last updated on March 19, 2024 pm

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]