Sorting Gene Expression Omnibus GSE file by phenoData

Question

[aok1234]

I was able to upload GSE40774 to R using:

gse40774 <- getGEO('GSE40774',GSEMatrix=TRUE)

show(gse40774)

I was also able to see the phenoData using:

show(pData(phenoData(gse40774[[1]]))[1:2,c(1:13)])

I am only interested in seeing those samples that have "hpv status: neg" in column 13 of the phenoData (characteristics_ch1.3). How do I filter the gse expression data by phenoData column?

Answer 1

[Basti]

You can easily select your samples of interest by searching the samples that match your criteria with which:

expr=exprs(gse40774[[1]])
pheno=pData(gse40774[[1]])

selection=rownames(pheno[which(pheno$characteristics_ch1.3=="hpv status: neg"),])

expr[,selection]