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

[Dykema, Karl]

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
>                              

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