[BioC] IQR implementation in varFiler and nsFilter (genefilter package)

[James F. Reid]

Dear list,

I have noticed that nsFilter and varFilter from the genefilter package 
implement their respective default variance function (var.func = IQR) in 
different ways and I don't know if this is intended or not. The IQR 
function in nsFilter uses an apply IQR on the rows of the matrix whereas 
varFilter uses its own rowIQRs function which lead to different results.
If this is intended I think it should be made clearer in the help page 
since both functions use the same default parameters for variance filtering.

Here is an example with the Biobase sample.ExpressionSet followed by 
it's sessionInfo()

Best,
James Reid.

 > library("Biobase")

Welcome to Bioconductor

   Vignettes contain introductory material. To view, type
   'openVignette()'. To cite Bioconductor, see
   'citation("Biobase")' and for packages 'citation(pkgname)'.

 > library("genefilter")
 >
 > data(sample.ExpressionSet)
 >
 > ## nsFilter using only var.filter
 > nsF <- nsFilter(sample.ExpressionSet,
+                 require.entrez = FALSE,
+                 remove.dupEntrez = FALSE,
+                 feature.exclude = FALSE)
 > varF <- varFilter(sample.ExpressionSet)
 >
 > nrow(nsF$eset) == nrow(varF)
Features
     TRUE
 > length(intersect(featureNames(nsF$eset), featureNames(varF)))
[1] 245
 > sessionInfo()

R version 2.9.0 (2009-04-17)
x86_64-redhat-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] genefilter_1.24.0 Biobase_2.4.1

loaded via a namespace (and not attached):
[1] annotate_1.22.0     AnnotationDbi_1.6.0 DBI_0.2-4
[4] RSQLite_0.7-1       splines_2.9.0       survival_2.35-4
[7] tools_2.9.0         xtable_1.5-5