Geo Data Matrix Using R

Question

[Yogesh Pandit]

I want something like,

ID   GB_ACC   Gene Title   Gene Symbol   ENTREZ_GENE_ID   GO_BP   GO_MF   GO_CC   Sample1   Sample2......

along with the corresponding values/IDs in the rows for a specific GSE. Following code gives me on the values for samples. How can I add rest of the information to the data matrix in R

library(GEOquery)
gse <- getGEO(filename = file)
probesets <- Table(GPLList(gse)[[1]])$ID
data.matrix <- do.call("cbind", lapply(GSMList(gse),
    function(x) {
        tab <- Table(x)
        mymatch <- match(probesets, tab$ID_REF)
        return(tab$VALUE[mymatch])
    }
                                       ))

And how do I restrict it to a few of my selected samples. Thanks in advance

Answer 1

[Stephen]

Use the GSEMatrix argument:

mygeomat <- getGEO("GSE12345", GSEMatrix=TRUE)

See page 13 of the docs.

[Sean Davis]

My words exactly.... Just a note that GSEMatrix=TRUE has been the default for almost two years.

[Sean Davis]

"mygeomat" in the answer above will be a list of ExpressionSet objects. Take a look at the Biobase vignette about ExpressionSets for details of subsetting and getting annotation information out.

Answer 2

[Larry_Parnell]

Via Simon Cockell's Twitter feed, I learned about GEO2R, a web app to analyze gene expression in GEO datasets using R. While this won't address your specific question, it may offer an alternate way to get the result you seek.