[BioC] Can\'t read canine CEL file with ReadAffy()

James W. MacDonald jmacdon at uw.edu
Mon Mar 18 21:06:56 CET 2013

Hi Kaj,

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
>> ReadAffy()
> 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,
> Kaj
>   -- output of sessionInfo():
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
> locale:
> [1] LC_COLLATE=Thai_Thailand.874  LC_CTYPE=Thai_Thailand.874
> [3] LC_MONETARY=Thai_Thailand.874 LC_NUMERIC=C
> [5] LC_TIME=Thai_Thailand.874
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] affy_1.36.1        Biobase_2.18.0     BiocGenerics_0.4.0
> loaded via a namespace (and not attached):
> [1] affyio_1.26.0         BiocInstaller_1.8.3   preprocessCore_1.20.0
> [4] zlibbioc_1.4.0
> --
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