[BioC] ReadAffy() Error - 2 Platforms in one file
Ovokeraye Achinike-Oduaran
ovokeraye at gmail.com
Thu May 10 13:11:41 CEST 2012
Hi all,
I get the following error when I try to get an affybatch object in the
code below. I understand that the Hu133a and Hu133b platforms were
used. When using getGEO, it's a bit more straightforward as I can
specify pData(phenoData(gse9006dat[[2]])) or
pData(phenoData(gse9006dat[[1]])) for the data I would like to analyse
but I can seem to figure it out with the raw data. Any help will be
greatly appreciated. Thanks.
-Avoks
> untar("GSE9006/GSE9006_RAW.tar", exdir="study2")
> celFiles = unlist(list.files("study2", full.names = TRUE))
> gse9006preset = ReadAffy(filenames = celFiles)
Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, :
Cel file study2/GSM254177.CEL.gz does not seem to be of HG-U133A type
R version 2.15.0 (2012-03-30)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_x.1252 LC_CTYPE=English_x.1252
[3] LC_MONETARY=English_x.1252 LC_NUMERIC=C
[5] LC_TIME=English_x.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] u133x3pcdf_2.10.0 ggplot2_0.9.0 u133x3p.db_2.7.1
[4] hgu133plus2.db_2.7.1 hgu95av2.db_2.7.1 hgu95a.db_2.7.1
[7] hgu133b.db_2.7.1 hgu133a.db_2.7.1 hu6800.db_2.7.1
[10] org.Hs.eg.db_2.7.1 RSQLite_0.11.1 DBI_0.2-5
[13] annotate_1.34.0 AnnotationDbi_1.18.0 limma_3.12.0
[16] affy_1.34.0 GEOquery_2.23.1 Biobase_2.16.0
[19] BiocGenerics_0.2.0
loaded via a namespace (and not attached):
[1] affyio_1.24.0 BiocInstaller_1.4.3 colorspace_1.1-1
[4] dichromat_1.2-4 digest_0.5.2 grid_2.15.0
[7] IRanges_1.14.2 MASS_7.3-17 memoise_0.1
[10] munsell_0.3 plyr_1.7.1 preprocessCore_1.18.0
[13] proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1.1
[16] reshape2_1.2.1 scales_0.2.0 stats4_2.15.0
[19] stringr_0.6 tools_2.15.0 XML_3.9-4.1
[22] xtable_1.7-0 zlibbioc_1.2.0
>
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