[BioC] Help with intcor() function

[Rob Scharpf]

> Message: 4
> Date: Sun, 29 Apr 2007 02:25:18 +0700
> From: " ????? ??????? " <kamushkina at gmail.com>
> Subject: [BioC] Help with intcor() function
> To: bioconductor at stat.math.ethz.ch
> Message-ID:
> 	<d1419f550704281225r76c93ac7y6561334a8297783d at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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

Hi Olga,

intCor() is part of the MergeMaid package.  Integrative correlation  
is an unsupervised method for obtaining a filtered set of features  
that are more reproducible, so it does not use the case-control  
variables in phenoData and you should not separate the cases from the  
controls.   The vignette and help page may a few examples you can  
follow:

http://www.bioconductor.org/packages/2.0/bioc/html/MergeMaid.html

Best regards,

Rob