[BioC] remove.dupEntrez from nsFilter{genefilter}

Klemens Vierlinger [guest] guest at bioconductor.org
Tue May 29 19:45:41 CEST 2012

Dear List,
I seem to have a problem with the nsFilter function. For genes which are represented by more than one probe, it should keep the probe with the highest IQR and delete the others. It seems to me that in the example below this is not the case.

Any ideas why?


con <- url('http://rdf.ait.ac.at/attachments/download/102/test.es')

# the expressionset test.es contains two probes for the ACT3 genes, where A_23_P160354 is the one with the highest IQR.
exprs(test.es)[fData(test.es)$ENTREZ %in% 10000, ]
apply(exprs(test.es)[fData(test.es)$ENTREZ %in% 10000, ], 1, IQR)

#However, if I apply nsFilter, the other Probe is kept 
remDup <- nsFilter(test.es, var.filter=F)$eset
featureNames(remDup)[fData(remDup)$ENTREZ %in% 10000]
exprs(remDup)[fData(remDup)$ENTREZ %in% 10000]

 -- output of sessionInfo(): 

> sessionInfo()
R version 2.13.2 (2011-09-30)
Platform: x86_64-pc-mingw32/x64 (64-bit)

[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

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

other attached packages:
[1] HsAgilentDesign026652.db_2.5.0 org.Hs.eg.db_2.5.0             RSQLite_0.10.0                 DBI_0.2-5                     
[5] AnnotationDbi_1.16.11          genefilter_1.34.0              Biobase_2.12.2                

loaded via a namespace (and not attached):
[1] annotate_1.30.1 IRanges_1.10.6  splines_2.13.2  survival_2.36-9 tools_2.13.2    xtable_1.6-0   

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