Dear Sean and all members,

I am trying to extract GSE data from GEO and do analysis. I am wondering if the GSE data has been normalized and log 2 transformed. R scripts and output are copied below.  Can somebody help me on this?

>Table(GSMList(gse)[[1]])[1:5, ]
     ID_REF       VALUE
1 1007_s_at 7.693888187
2   1053_at 8.571408272
3    117_at 5.179812431
4    121_at 7.468027592
5 1255_g_at 3.118550777
> Columns(GSMList(gse)[[1]])[1:5, ]
     Column                Description
1    ID_REF
2     VALUE log2 signal intensity, RMA       <<<<< Does this means that the value is log2 transformed and the data was         normalized by RMA
NA     <NA>                       <NA>
NA.1   <NA>                       <NA>
NA.2   <NA>                       <NA>

According to GEOquery package I should do following steps in order to get the eset:

> 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])
+ }))
> data.matrix <- apply(data.matrix, 2, function(x) {
+ as.numeric(as.character(x))
+ })
> data.matrix <- log2(data.matrix)
> data.matrix[1:5, ]

     GSM424759 GSM424760 GSM424761 GSM424762 GSM424763 GSM424764 GSM424765
[1,]  2.943713  2.917086  2.926155  2.983485  2.973219  2.962445  2.926030
[2,]  3.099532  3.136898  3.152696  3.217172  3.206948  3.198448  3.135146
[3,]  2.372900  2.309177  2.354380  2.373350  2.368464  2.381139  2.314555
[4,]  2.900727  2.873853  2.863911  2.879232  2.927384  2.913594  2.852870
[5,]  1.640876  1.645330  1.494274  1.792643  1.719597  1.648126  1.605055

Is the log2 transformation  necessary for this dataset?
Many thanks

Jing


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