GSE experiment has two platforms, how to find GSM files specific to one platform without using GEOMetadb
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?
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Shicheng Guo
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grokaine •
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grokaine •
2 answers
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)
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Shicheng Guo
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.
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Sean Davis
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