[BioC] GEOquery: GDS2MA failure

[Philipp Pagel]

	Hi!

I am trying to analyze some GEO data and have been facing download problems
which I was able to fix by reading recent postings on this list. But something
goes wrong when I try to convert to an MAList. I suspect it could have
something to do with the fact that this particular data series comprizes two
different platforms. 

Here the transcript of what I do:

-------------------------------------------------------------------
require(GEOquery)
options(download.file.method="wget") # fix download problem
dat <- getGEO(filename='data/GSE6794_family.soft.gz', destdir=datapath, GSEMatrix=F)
# [...] some logging output, no errors or warnings

MA <- GDS2MA(dat,do.log2=T)
Loading required package: limma
File stored at: 
/tmp/RtmpvL1wBp/GPL75.annot.gz/tmp/RtmpvL1wBp/GPL76.annot.gz
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "Table", for signature "GSE"
In addition: Warning messages:
1: In if (GSEMatrix & geotype == "GSE") { :
  the condition has length > 1 and only the first element will be used
2: In if (geotype == "GDS") { :
  the condition has length > 1 and only the first element will be used
3: In if (geotype == "GSE" & amount == "full") { :
  the condition has length > 1 and only the first element will be used
4: In if (geotype == "GSE" & amount != "full" & amount != "table") { :
  the condition has length > 1 and only the first element will be used
5: In if (geotype == "GPL") { :
  the condition has length > 1 and only the first element will be used
6: In if (geotype == "GSM") { :
  the condition has length > 1 and only the first element will be used
7: In if (!file.exists(destfile)) { :
  the condition has length > 1 and only the first element will be used
8: In gzfile(fname, open = "rt") :
  only first element of 'description' argument used
9: In gzfile(fname, open = "rt") :
  only first element of 'description' argument used

sessionInfo()
R version 2.11.1 (2010-05-31) 
x86_64-pc-linux-gnu 

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C              LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8    LC_PAPER=en_US.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C            LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  utils     datasets  grDevices methods   base     

other attached packages:
[1] limma_3.4.0     GEOquery_2.13.5 Biobase_2.8.0   lattice_0.18-8 

loaded via a namespace (and not attached):
[1] grid_2.11.1 RCurl_1.4-2 XML_3.1-0  
-------------------------------------------------------------------


I can use GSMList to extract a list with all GSM entries but, of course, GDS2MA
will not work on a list and I would have to run it on all list members
individually which I will have to re-assemble into a single MA object
somehow... Any hints welcome.

cu
	Philipp 

-- 
Dr. Philipp Pagel
Lehrstuhl für Genomorientierte Bioinformatik
Technische Universität München
Wissenschaftszentrum Weihenstephan
Maximus-von-Imhof-Forum 3
85354 Freising, Germany
http://webclu.bio.wzw.tum.de/~pagel/