[BioC] error preProcessGeneST ArrayTools (R 2.15.2, BioC 2.11)

[James W. MacDonald]

Hi Jose,

On 12/20/2012 12:20 PM, José LÓPEZ wrote:
> Dear all,
>
> I was trying to use preProcessGeneST ArrayTools to get rid of control probes in Mouse Gene 1.0ST arrays, but it dosent work in last R/BioC version.
> It was working perfectly in previous R/BioC version. Do I downgrade to previous version to continue to use the ArrayTools package?
> It is possible that the error has a different cause?

This looks like a bug in the current version of the 
mogene10sttranscriptcluster.db package, as the MAP object appears to be 
missing:

 > ls(2)
  [1] "mogene10sttranscriptcluster"
<snip>
[20] "mogene10sttranscriptclusterGO2ALLPROBES"
[21] "mogene10sttranscriptclusterGO2PROBE"
[22] "mogene10sttranscriptclusterMAPCOUNTS"
[23] "mogene10sttranscriptclusterMGI"
<snip>

So I don't think downgrading anything will help - we just need to 
rebuild this package.

But this brings me to a different question. The function you are using 
is intended to annotate things and then output in the current directory, 
and removing control probes is just a side effect of one argument. So 
are you trying to annotate, or to remove control probes?

If you just want to remove control probes, note that you can do

 > data(mogene10stCONTROL)

and then you can subset your eset using the resulting data.frame:

eset_no_control <- eset_norm[!featureNames(eset_norm) %in% 
mogene10stCONTROL$probeset_id,]

Note the use of the bang (!) preceding featureNames - we want to remove 
these things, not select for them.

Best,

Jim


>
> Thank you for your kind help,
>
>> eset_process = preProcessGeneST(eset_norm, output = TRUE)
> Warning message:
> In chkPkgs(chip) :
>    The mogene10sttranscriptcluster.db package does not appear to contain annotation data.
> Error in function (x, envir, mode = "any", ifnotfound = list(function(x) stop(paste0("value for '",  :
>    error in evaluating the argument 'envir' in selecting a method for function 'mget': Error: object 'mogene10sttranscriptclusterMAP' not found
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] mogene10stv1cdf_2.11.0               annaffy_1.30.0                       KEGG.db_2.8.0
>   [4] GO.db_2.8.0                          arrayQualityMetrics_3.14.0           ArrayTools_1.18.0
>   [7] mogene10sttranscriptcluster.db_8.0.1 org.Mm.eg.db_2.8.0                   RSQLite_0.11.2
> [10] DBI_0.2-5                            affy_1.36.0                          annotate_1.36.0
> [13] AnnotationDbi_1.20.3                 vsn_3.26.0                           Biobase_2.18.0
> [16] BiocGenerics_0.4.0                   limma_3.14.3
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.26.0         affyPLM_1.34.0        beadarray_2.8.1       BeadDataPackR_1.10.0  BiocInstaller_1.8.3
>   [6] Biostrings_2.26.2     Cairo_1.5-2           cluster_1.14.3        colorspace_1.2-0      gcrma_2.30.0
> [11] genefilter_1.40.0     grid_2.15.2           Hmisc_3.10-1          hwriter_1.3           IRanges_1.16.4
> [16] lattice_0.20-10       latticeExtra_0.6-24   parallel_2.15.2       plyr_1.8              preprocessCore_1.20.0
> [21] RColorBrewer_1.0-5    reshape2_1.2.2        setRNG_2011.11-2      splines_2.15.2        stats4_2.15.2
> [26] stringr_0.6.2         survival_2.37-2       SVGAnnotation_0.93-1  tools_2.15.2          XML_3.95-0.1
> [31] xtable_1.7-0          zlibbioc_1.4.0
>> class(H2Bgfp_norm)
> [1] "ExpressionSet"
> attr(,"package")
> [1] "Biobase"
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099