[BioC] Creating a customized cut flow with the affy/limma packages

[J.M.Jensen [guest]]

Dear all,
I am trying to create a customized cut flow with the affy/limma packages. In order to assign different cut-off values between different arrays would be to first make one cut-off and then use the remaining expression set in further analysis. When working with the affy/limma packages, I read and normalize my data with the justRMA() function, fit a linear model with the limma package and use the decideTests() from the limma package to select probes with a specified cut-off (e.g. lfc). The problem is that I cannot assign multiple criteria for the cut flow. For example, if I want to remove all probes from my data set that differ more than a lfc of 1.2 between two controls, regardless of the expression values in the rest of the samples. After this cut, I would then be able to use another cut off value, e.g. lfc=1.8 to select probes from different contrasts of the remaining data. I tried looking into the vennSelect() (affycoretools), because I can use it to select various contrasts 
 and their intersection, however, I cannot figure how to assign different cut off criteria. 
Any help or thoughts on this would be most appreciated.
Best regards,
J.M. Jensen

 -- output of sessionInfo(): 

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

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] venneuler_1.1-0      rJava_0.9-3          affycoretools_1.24.0
 [4] KEGG.db_2.5.0        gplots_2.10.1        KernSmooth_2.23-4   
 [7] caTools_1.12         bitops_1.0-4.1       gdata_2.8.2         
[10] gtools_2.6.2         GO.db_2.5.0          hgu133plus2.db_2.5.0
[13] org.Hs.eg.db_2.5.0   RSQLite_0.9-4        DBI_0.2-5           
[16] hgu133plus2cdf_2.8.0 annotate_1.30.1      AnnotationDbi_1.14.1
[19] limma_3.8.3          affy_1.30.0          Biobase_2.12.2      

loaded via a namespace (and not attached):
 [1] affyio_1.20.0         annaffy_1.24.0        biomaRt_2.8.1        
 [4] Biostrings_2.20.4     Category_2.18.0       gcrma_2.24.1         
 [7] genefilter_1.34.0     GOstats_2.18.0        graph_1.30.0         
[10] GSEABase_1.14.0       IRanges_1.10.6        preprocessCore_1.14.0
[13] RBGL_1.28.0           RCurl_1.6-10.1        splines_2.13.0       
[16] survival_2.36-5       tools_2.13.0          XML_3.4-2.2          
[19] xtable_1.6-0     

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