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

[Paul Geeleher]

Ok thanks Martin that worked. That was rather stupid of me, apologies
for wasting everyones time!

On Sat, Oct 9, 2010 at 6:22 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 10/09/2010 10:01 AM, Paul Geeleher wrote:
>> 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
>
> These are not the correct versions of affy & Biobase for your R, see
>
> http://bioconductor.org/install/index.html#update-bioconductor-packages
>
> for update
>
> and
>
> http://bioconductor.org/help/bioc-views/release/bioc/
>
> for released software (and their versions, on the individual package pages)
>
> ReadAffy() works for me with this sessionInfo():
>
>> sessionInfo()
> R version 2.11.1 Patched (2010-08-30 r52862)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] affy_1.26.1   Biobase_2.8.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.16.0         preprocessCore_1.10.0
>> ReadAffy("5500024030700072107989.G03.CEL")
> AffyBatch object
> size of arrays=744x744 features (16 kb)
> cdf=HT_HG-U133A (22277 affyids)
> number of samples=1
> number of genes=22277
> annotation=hthgu133a
> notes=
>>
>
>
> Martin
>
>>
>> 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
>>>
>>
>>
>>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>



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