[BioC] Help with intcor() function

[Ольга Камнева]

Hi, all,

I need some suggestions =)

I'd like to use package metaArray to perform meta-analysis.
One of  the tools of this package is integrative correlation analysis
(proposed Parmigiani et al. in 2004), it allows to evaluat concordance
of genes expression between studies.
The main function is intcor() which allows to get integrative
correlations, then I can filter genes (reject genes that is
uncorrelated between studies), argument of intcor()  function is
merged object, combination of exprSet (package affy).
I have different samples in exprSet (case and control). Should I
separate case-samples from control-samples before analysis?
Or intcor() function can distinguish samples (maybe it gets
information from phenoData slots of exprSets...)

Thanks a lot,
Olga