[BioC] Error reading cel files using Readaffy() or getGEO()
Salwa [guest]
guest at bioconductor.org
Mon Feb 6 20:01:18 CET 2012
I have been trying to read cel files from NCBI website and have been having problems. I was able to read the cel files using getGEO() using R version 2.14.0 but the problem is i need the matchprobe library which only works under R version 2.11. So i switched to R version 2.11 but I just keep getting the following error using the getGEO() : Error in validObject(.Object) :
invalid class "ExpressionSet" object: featureNames differ between assayData and featureData. So instead i tried using the Readaffy() from the affy() library but i got the following error: cannot allocate vector of size 470.1. I tried increasing the memory using the memory.size() but it doesn't work. I have alot of space on the directory. If i use the rma, it will get the expressions and perform rma and i don't want that.
Any help or any ideas to get one of them working?
-- output of sessionInfo():
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
[3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] affy_1.26.1 GEOquery_2.13.7 Biobase_2.8.0
loaded via a namespace (and not attached):
[1] affyio_1.16.0 preprocessCore_1.10.0 RCurl_1.4-2
[4] tools_2.11.1 XML_3.2-0
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