[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.


> 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)

[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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