dear Bioc,


I want to use GEOquery to get a GSE dataset corresponding to two GPL. when I
use the following code I retrive an incompleate expression set, how can i
solve the problem?

>library(GEOquery)
>gse <- getGEO("GSE3494", GSEMatrix = FALSE)
>if (.Platform$OS.type != "windows") {
>    gse <- getGEO("GSE3494", GSEMatrix = TRUE)
>    show(gse)
>    show(pData(phenoData(gse[[1]]))[1:5, c(1, 6, 8)])
>}
>gsmplatforms <- lapply(GSMList(gse), function(x) {
>    Meta(x)$platform
>})
>probsets <- Table(GPLList(gse)[[1]])$ID
>    data.matrix <- log2(do.call("cbind", lapply(GSMList(gse), function(x) {
>    tab <- Table(x)
>    mymatch <- match(probesets, tab$ID_REF)
>    return(tab$VALUE[mymatch])
>})))
>data.matrix[1:5, ]
>require(Biobase)
>rownames(data.matrix) <- probesets
>colnames(data.matrix) <- names(GSMList(gse))
>pdata <- data.frame(samples = names(GSMList(gse)))
>rownames(pdata) <- names(GSMList(gse))
>pheno <- as(pdata, "AnnotatedDataFrame")
>eset2 <- new("ExpressionSet", exprs = data.matrix, phenoData = pheno)
>eset2

thank you
          john

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