[BioC] GEO and Limma
Freudenberg, Johannes (NIH/NIEHS) [E]
johannes.freudenberg at nih.gov
Tue Oct 4 17:33:50 CEST 2011
Hi Avoks,
> I can hardly figure out how to get from the expression set to the analysis...
I can't tell what the problem is but my best guess would be that you're dealing with a list here. Each list element correspond to a different platform. So all you need to do is something like
> myGSEeset <- gse25724dat[[1]]
> head(exprs(myGSEeset))
etc...
I hope this helps. Please feel free to post more specific questions if it doesn't.
Best,
Johannes
-----Original Message-----
From: Ovokeraye Achinike-Oduaran [mailto:ovokeraye at gmail.com]
Sent: Tuesday, October 04, 2011 10:28 AM
To: bioconductor at r-project.org
Subject: [BioC] GEO and Limma
Hi all,
I've been struggling a bit with GEO and limma. I've come up with 2 questions that I'ld appreciate some input on.
Question 1:
I have a design matrix with 6columns for an expression set with 3
columns(3 levels, 2 agents). How do I create a model matrix to fit my design matrix for this dataset (eg. gds3715 below)? For a straight forward single factor analysis eg. gds161, the code below seems to work fine.
gds161dat = getGEO('GDS161',destdir=".") gds161eset = GDS2eSet(gds161dat, do.log2=TRUE) m = pData(gds161eset)$metabolism
design_gds161 = createDesignMatrix(gds161eset)
design_gds161 = model.matrix(~m)
fit = lmFit(gds161eset, design_gds161)
fit2 = eBayes(fit)
results = topTable(fit2, adjust ="BH", number = nrow(gds161eset)) excel = write.table(results, file = file.choose(), sep = ",")
gds3715dat = getGEO('GDS3715',destdir=".") gds3715eset = GDS2eSet(gds3715dat, do.log2=TRUE) DIR = paste(pData(gds3715eset)$disease.state,
pData(gds3715eset)$agent, sep =".")
m = data.frame("fac1" = pData(gds3715eset)$disease.state, "fac2" =
pData(gds3715eset)$agent)
design_gds3715 = createDesignMatrix(gds3715eset)
design_gds3715 = model.matrix(~m)
fit = lmFit(gds3715eset, design_gds3715)
fit2 = eBayes(fit)
results = topTable(fit2, adjust ="BH", number = nrow(gds3715eset)) excel = write.table(results, file = file.choose(), sep = ",")
Question 2:
How can I run a similar (limma) analysis with GSE files?
I can hardly figure out how to get from the expression set to the analysis...I've read the Using the GEOquery Package documentation several times over. I'm just have a hard time getting it to work.
gse25724dat = getGEO('GSE25724', GSEMatrix = TRUE)
This is supposed to give me an expressionset, I can't seem to figure out how to analyze it with limma.
Please help.
Thanks.
Avoks
sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_xxx. LC_CTYPE=English_xxx [3] LC_MONETARY=English_xxx LC_NUMERIC=C [5] LC_TIME=English_xxx
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] puma_2.4.0 mclust_3.4.10 affy_1.30.0 limma_3.8.3
[5] GEOquery_2.19.4 Biobase_2.12.2
loaded via a namespace (and not attached):
[1] affyio_1.20.0 preprocessCore_1.14.0 RCurl_1.6-10.1
[4] tools_2.13.1 XML_3.4-2.2
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