[BioC] ReadAffy() Error - 2 Platforms in one file

[Ovokeraye Achinike-Oduaran]

Hi Sean,

I realize that from the error but I'm not quite sure how to go about
processing it, hence the request for help on how to go about it.
That's why I had said that the getGEO() is a bit more straightforward.

Thanks.

-Avoks

On Thu, May 10, 2012 at 1:35 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>
> On Thu, May 10, 2012 at 7:11 AM, Ovokeraye Achinike-Oduaran
> <ovokeraye at gmail.com> wrote:
>>
>> 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
>>
>
> You'll need to process the HG-U133A and HG-U133B files separately.  ReadAffy
> is just telling you that.
>
> Sean
>
>>
>>
>>
>> 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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>
>