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oligo：geo-arrayexpress芯片数据处理.md

oligo：geo-arrayexpress芯片数据处理.md 11 KB
Постійне посилання Історія Запис

title: oligo：GEO/ArrayExpress芯片数据处理 tags: [] id: '2165' categories:

  • - 数据库
  • - 数据清洗 comments: false date: 2022-07-29 18:15:10 ---

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
  • 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

  • f_dedup_IQR 函数来源
  • 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]

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