[BioC] problem with nsFilter and hthgu133a format eset

[Marc Carlson]

Hi Fraser,

I am afraid that you are unlucky on this one.  The probe sequence that
is coming up as not found is a newly added control sequence from
Affymetrix (added this June).  So it was not in the Affy files when we
made the annotation package back in April.  A newer package IS available
however in the development branch right now.  So you can use it today if
you install R-devel and use biocLite().  Alternatively, you could wait a
few weeks for the new release of R and bioconductor to go out.  But
whatever you do, do not attempt to use the newer annotation packages
with the older version of Bioconductor.  That will definitely NOT work. 

But installing a new R might be kind of a pain for you and its not your
fault that Affy pulled a fast one on us.  So I did some quick work for
you to determine that the following probes are expected to be "extras"
(because they were added by Affy last June).

[1] "AFFX-BioB-3_at"  "AFFX-BioB-5_at"  "AFFX-BioB-M_at"  "AFFX-BioC-3_at"
[5] "AFFX-BioC-5_at"  "AFFX-BioDn-3_at" "AFFX-BioDn-5_at" "AFFX-CreX-3_at"
[9] "AFFX-CreX-5_at"

So as a work around, I am betting that you probably just want to use the
subset operator to remove those probes out of your ExpressionSet object
before proceeding.

Hope this helps,


  Marc




Fraser Sim wrote:
> Hi,
>
> I am having a problem running the following code which utilizes an eset
> derived from hthgu133a CEL files.
>
>   
>> eset
>>     
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 13834 features, 9 samples 
>   element names: exprs, se.exprs 
> phenoData
>   sampleNames: <<masked>>  (9 total)
>   varLabels and varMetadata description:
>     sample: arbitrary numbering
>     CEL: NA
>     phenotype: NA
>     ShortName: NA
> featureData
>   featureNames: 1007_s_at, 1053_at, ..., AFFX-r2-Ec-bioD-5_at  (13834 total)
>   fvarLabels and fvarMetadata description: none
> experimentData: use 'experimentData(object)'
> Annotation: hthgu133a
>
>   
>> library(genefilter)
>> nsF = nsFilter(eset, var.filter = FALSE)$eset
>>     
> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : 
>   value for "AFFX-BioB-3_at" not found'
>
>   
>> sessionInfo()
>>     
> R version 2.9.1 (2009-06-26) 
> i386-pc-mingw32 
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] grid      stats     graphics  grDevices datasets  utils     methods  
> [8] base     
>
> other attached packages:
>  [1] RODBC_1.2-5         bioDist_1.16.0      KernSmooth_2.23-2  
>  [4] hthgu133a.db_2.2.11 RSQLite_0.7-1       DBI_0.2-4          
>  [7] AnnotationDbi_1.6.1 genefilter_1.24.2   RColorBrewer_1.0-2 
> [10] gplots_2.7.1        caTools_1.9         bitops_1.0-4.1     
> [13] gdata_2.4.2         gtools_2.6.1        Biobase_2.4.1      
> [16] rcom_2.2-1          rscproxy_1.3-1     
>
> loaded via a namespace (and not attached):
> [1] annotate_1.22.0 splines_2.9.1   survival_2.35-4 xtable_1.5-5   
>
> The code works as expected using an eset derived from hgu133plus2 CEL files.
>
> Cheers,
> Fraser
>
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