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

[Ovokeraye Achinike-Oduaran]

Thanks Sean. I guess I was looking for an easier way out. But all
sorted. Thanks.

-Avoks

On Thu, May 10, 2012 at 1:46 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>
> On Thu, May 10, 2012 at 7:41 AM, Ovokeraye Achinike-Oduaran
> <ovokeraye at gmail.com> wrote:
>>
>> 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.
>>
>
> You will need to determine which .CEL files are from the U133A platform and
> which are from the U133B platform.  Then, you'll want to use those lists of
> CEL file names to call ReadAffy once for each list.  It will be up to you to
> combine the results into one ExpressionSet after your normalization is
> complete for both platforms.
>
> Hope that helps clarify things a bit.
>
> Sean
>
>
>>
>> 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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>> >
>>
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>
>