[BioC] Error reading cel files using Readaffy() or getGEO()

[James W. MacDonald]

Hi Salwa,

On 2/6/2012 2:01 PM, Salwa [guest] wrote:
>    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?

I doubt you need the matchprobes package. What exactly are you trying to do?

Best,

Jim


>
>   -- 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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>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

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