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

[Martin Morgan]

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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>>
>> --
>> 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