[BioC] Problem with ReadAffy and Connectivity Map .CEL files

[James W. MacDonald]

Hi Karl,

Fixed in devel and release versions. This will propagate normally 
through the build system and be available tomorrow or the next day or so 
(versions 1.24.2 for release and 1.25.2 for devel), or for the impatient 
they can be downloaded and built from svn.

Best,

Jim



Dykema, Karl wrote:
> Hello all, 
> 
> I am having troubles reading in some CEL files from the Broad Connectivity Map. (http://www.broadinstitute.org/cmap/) Some of the files seem to work fine, but when I try to load a file with the chip type "HT_HG-U133A_EA" I receive me this error message:
> 
> 
>> ReadAffy(filenames=tf[1:2])
> Error in value[[3L]](cond) :
>   row names supplied are of the wrong length
>   AnnotatedDataFrame 'initialize' could not update varMetadata:
>   perhaps pData and varMetadata are inconsistent?
> 
> 
> The specific files I am trying to read in this example are "5202764005790181113004.H02.CEL" and "5202764005790181113004.H03.CEL". I was able to find another bioC mailing list thread describing issues with other arrays of this type, but they were able to load the files without any problems using ReadAffy. I would appreciate any suggestions or advice! Thanks in advance.
> 
> 
> 
> -------------------------------------------
> Karl Dykema
> Computational Biologist
> Van Andel Research Institute
> 333 Bostwick Ave NE
> Grand Rapids, MI 49503
> 616-234-5554
> 
> 
> 
>> sessionInfo()
> R version 2.10.0 (2009-10-26)
> x86_64-unknown-linux-gnu
> 
> 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] PGSEA_1.14.0        reb_1.20.0          idiogram_1.22.0
>  [4] plotrix_2.7-2       annotate_1.24.0     AnnotationDbi_1.8.0
>  [7] limma_3.2.1         affy_1.24.0         Biobase_2.6.0
> [10] gtools_2.6.1        gdata_2.6.1
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0        DBI_0.2-4            preprocessCore_1.8.0
> [4] RSQLite_0.7-3        tools_2.10.0         xtable_1.5-5
>>                              
> 
> This email message, including any attachments, is for th...{{dropped:6}}
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826