[BioC] How remove controls probes - Affymetrix Gene

[Sophie Lamarre [guest]]

Hello,

I work on affymetrix mouse gene 1.0 ST.

I want to know how remove controls probes on Affymetrix Gene.
In my studie, I downloaded two files on Affymetrix website:
- The Probeset Annotations, CSV Format, Release 32
 file (NetAffx Analysis Center -> Exon/Gene -> NetAffy Query -> "Mouse Gene 1.0 ST")
- The Transcript Cluster Annotations, CSV, Release 32 file (NetAffx Analysis Center -> Exon/Gene -> NetAffy Query -> "Mouse Gene 1.0 ST")

With the first, I had 28 856 main probesets and with second 28 350 main probesets.

I add that I run a RMA option "core" with the oligo package. I just want a probe for a probeset.

Which file I have to use? (I did'nt use the command getNetAffy because I realized that I lost more probesets! (There were only 28 270 main probes)). 

Thank you for advance for your answer and your help.

Sophie LAMARRE

 -- output of sessionInfo(): 

R version 2.13.0 (2011-04-13)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252    LC_MONETARY=French_France.1252
[4] LC_NUMERIC=C                   LC_TIME=French_France.1252    

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pd.mogene.1.0.st.v1_3.2.0 oligo_1.16.2              preprocessCore_1.14.0    
 [4] GOstats_2.18.0            RSQLite_0.9-4             DBI_0.2-5                
 [7] graph_1.30.0              Category_2.18.0           genefilter_1.34.0        
[10] gplots_2.8.0              caTools_1.12              bitops_1.0-4.1           
[13] gdata_2.8.2               gtools_2.6.2              geneplotter_1.30.0       
[16] lattice_0.19-23           annotate_1.30.0           AnnotationDbi_1.14.1     
[19] RColorBrewer_1.0-5        ArrayTools_1.12.0         affy_1.30.0              
[22] limma_3.8.3               oligoClasses_1.14.0       Biobase_2.12.2           

loaded via a namespace (and not attached):
 [1] affxparser_1.24.0 affyio_1.20.0     Biostrings_2.20.3 bit_1.1-7         ff_2.2-3         
 [6] GO.db_2.5.0       GSEABase_1.14.0   IRanges_1.10.6    RBGL_1.28.0       splines_2.13.0   
[11] survival_2.36-5   tools_2.13.0      XML_3.4-2.2       xtable_1.5-6 

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