Question: Importing with GEOquery selected GSMs
2
gravatar for orzech_mag
4.2 years ago by
orzech_mag190
Poland/Łódź
orzech_mag190 wrote:

Hallo,

I have some problem with importing data using GEOquery. I download an ExpressionSet for some further analysis, however in my record only few GSMs from all are interesting for me. My question is how to modify my code to download only the selected GSMs and analyze it further with limma package. I am grateful for any suggestions.

eset<-getGEO('GSE13937')[[1]] -----> but I would like the data only for e.g. GSM26056, GSM26076, GSM26102, and GSM26123

And, then perform a standard analysis like:

design <-cbind(normal=c(1,1,0,0),
              tumour=c(0,0,1,1))
c <-makeContrasts(normal-tumour,levels=design)
fit <-lmFit(eset, design)
fit2 <-contrasts.fit(fit,c)
fit2 <-eBayes(fit2)
glist <-topTable(fit2, n=50, adjust="BH", sort.by="P", p.value=0.01)​
genomics R geo • 1000 views
ADD COMMENTlink modified 4.2 years ago by Sean Davis25k • written 4.2 years ago by orzech_mag190
1
gravatar for Sean Davis
4.2 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

Well, subsetting an ExpressionSet is pretty easy:

eset1=eset[,c("GSM426056", "GSM426076", "GSM426102", "GSM426123")]

However, you might not want to do things this way.  Instead, you can create your design matrix with all "0" except for the two "normals" and the two "tumors".  The rest of your code can remain unchanged (the contrasts, testing, etc.).  You get the benefit of a more robust measure of variance if you include all samples even though the testing will be based on only your four samples.

ADD COMMENTlink written 4.2 years ago by Sean Davis25k

Thank you for help!

ADD REPLYlink written 4.2 years ago by orzech_mag190
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