[BioC] Can\'t read canine CEL file with ReadAffy()
James W. MacDonald
jmacdon at uw.edu
Mon Mar 18 21:06:56 CET 2013
You can try two things. First, check to see if this is the first file
that you are trying to read. If so, there might have been a problem when
you downloaded, so you might try re-downloading.
Second, if it is not the first file, you might have a non-canine file in
the bunch. You could try moving it to its own directory, read it in
alone using ReadAffy() and then see what kind of celfile it is.
On 3/17/13 6:25 AM, Kaj Chokeshaiusaha [guest] wrote:
> Dear R helpers,
> I would like to note in the first place that I'm very naive to R. So I must apologize you all in advance if my problem is too simple. Hope you will accept my apology.
> I can't read CEL files of canine bone cancers with 'ReadAffy()'.
> Would you please suggest me what happens and what I should try next?
> R shows me this error
> Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, :
> Cel file D:/Canine Osteosarcoma/GSM596543.CEL does not seem to have the correct dimensions
> Best Regards,
> -- output of sessionInfo():
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>  LC_COLLATE=Thai_Thailand.874 LC_CTYPE=Thai_Thailand.874
>  LC_MONETARY=Thai_Thailand.874 LC_NUMERIC=C
>  LC_TIME=Thai_Thailand.874
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  affy_1.36.1 Biobase_2.18.0 BiocGenerics_0.4.0
> loaded via a namespace (and not attached):
>  affyio_1.26.0 BiocInstaller_1.8.3 preprocessCore_1.20.0
>  zlibbioc_1.4.0
> Sent via the guest posting facility at bioconductor.org.
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