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}}

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}} > > _______________________________________________ > 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 -- 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