[BioC] GEO and Limma

[Freudenberg, Johannes (NIH/NIEHS) [E]]

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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