GSE experiment has two platforms, how to find GSM files specific to one platform without using GEOMetadb

Question

[grokaine]

How to list the GSM files specific to one GPL number and to one GSE ID?

I can do this with GEOMetadb but it seems offhand, can't it be done from GEOQuery?

Answer 1

[Shicheng Guo]

Here, I can show you an example with GSE49604 which included two platforms: GPL10558 and GPL8432. Below is the solution:

library("GEOquery")

GSE49604 <- getGEO("GSE49604")
GSE49604

data1 <- as.data.frame(exprs(GSE49604[[1]]))
phen1 <- pData(phenoData(GSE49604[[1]]))

data2 <- as.data.frame(exprs(GSE49604[[2]]))
phen2 <- pData(phenoData(GSE49604[[2]]))

head(data1)
head(data2)

Answer 2

[Sean Davis]

GEOquery takes care of this for you by returning a list of two ExpressionSets (when two platforms are involved). You can interrogate those objects to get the GSMs for each platform using sampleNames, for example.