[BioC] Creating a customized cut flow with the affy/limma packages
J.M.Jensen [guest]
guest at bioconductor.org
Mon Feb 13 15:35:40 CET 2012
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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