2025-03-11
pacman::p_load("Biobase","GEOquery")
gcel = getGEOSuppFiles("GSE20986")
The directory GSE20986 has been created.
setwd("GSE20986/") system("tar xvf GSE20986_RAW.tar") gse20986raw = affy::ReadAffy() setwd("../") system("rm -fr GSE20986")
tissue = factor(c(1,2,2,1,2,1,3,3,3,4,4,4),levels = 1:4, labels=c("iris","retina","choroides","huvec")) pd = data.frame(tissue) rownames(pd) = colnames(gse20986raw) pData(gse20986raw) = pd
The normalization is performed using the method GC-RMA.
pacman::p_load("gcrma","hgu133plus2probe") gse20986 = gcrma(gse20986raw)
pacman::p_load(hgu133plus2.db) a = AnnotationDbi::select(hgu133plus2.db,keys=featureNames(gse20986), columns=c("ENTREZID","ENSEMBL","GO"),keytype="PROBEID") b = BiocGenerics::match(featureNames(gse20986),a[,"PROBEID"]) fData(gse20986) = a[b,]
save(gse20986,file="gse20986.rda")