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

[José López]

Hi Jim,

Thank you for your quick reply and your useful explanation.
In fact, I was using the function to subset the eset since I didn’t  
know other way to do it (before).

By the way, I would like to know your opinion about whether is a good  
option to filter controls before doing moderate t-statistics (limma)  
or should I rather perform statistic on the whole variable dataset  
(including controls)?

I have read in that in contrast to standard t-statistic, common filter/ 
test pairs does not necessarily translate in power gains when  
moderated t-statistics is performed (Bourgon, Gentleman and Huber,  
2009), so following their indications, I don’t use to apply any filter  
on genes. The question is whether you think it is a good practice to  
remove control probes (not genes) or not.

Sorry if the question is not clearly exposed.

Thank you in advance for your time and your help.

Best,

Jose

El dic 20, 2012, a las 7:00 p.m., James W. MacDonald escribió:

> 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
>