[BioC] ReadAffy() can't read CEL files from TCGA...

[Paul Geeleher]

Apologies for the lack of info, I thought there'd probably be
something very obvious I was doing wrong.

These files are from the BI__HT_HG-U133A archive of the glioblastoma dataset.

I've uploaded one of the files here:
frink.nuigalway.ie/~pat/5500024030700072107989.G03.CEL


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

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

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

other attached packages:
[1] affy_1.24.0   Biobase_2.6.0

loaded via a namespace (and not attached):
[1] affyio_1.14.0        preprocessCore_1.8.0
>






On Fri, Oct 8, 2010 at 10:03 PM, Tim Triche <tim.triche at gmail.com> wrote:
> Post the URL from which you are downloading them.
> Depending on the format, level, etc. the data can be totally different from
> what Bioconductor would expect.
>
> On Fri, Oct 8, 2010 at 9:57 AM, Paul Geeleher <paulgeeleher at gmail.com>
> wrote:
>>
>> Hi,
>>
>> I downloaded some glioblastoma hg-u133a CEL files from The Cancer
>> Genome Atlas (http://cancergenome.nih.gov/) and ReadAffy() can't seem
>> to load the files. The CEL files are only 5.3 megs each so maybe they
>> are compressed or something? And when you open them they look like
>> binary files?
>>
>> I'm wondering if anybody knows what kind of files these are and how I
>> might read them? ReadAffy() gives the following error:
>>
>> > a <- ReadAffy()
>> Error in value[[3L]](cond) :
>>  row.names should specify one of the variables
>>  AnnotatedDataFrame 'initialize' could not update varMetadata:
>>  perhaps pData and varMetadata are inconsistent?
>>
>>
>> --
>> Paul Geeleher
>> School of Mathematics, Statistics and Applied Mathematics
>> National University of Ireland
>> Galway
>> Ireland
>> --
>> www.bioinformaticstutorials.com
>>
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>
>
>
> --
> With four parameters I can fit an elephant, and with five I can make him
> wiggle his trunk.
> John von Neumann
>



-- 
Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com