[BioC] inSilicoMerging:::mergeCOMBAT covariates

Quentin De Clerck qdeclerc at vub.ac.be
Wed Apr 30 17:49:00 CEST 2014

Hi François,

I am sorry for the confusion. Indeed the package do not handle covariates, but we plan to integrate this in next release. In the meantime I suggest you to take a look at the BatchAdjust method in the latest SCAN.UPC package.

Kind regards,

Quentin De Clerck

Le 28 avr. 2014 à 20:34, François Lefebvre <lefebvrf at gmail.com> a écrit :

> Hi,
> I was testing the package inSilicoMerging, particularly to perform the
> COMBAT batch effect removal.
> The original paper
> http://www.biomedcentral.com/1471-2105/13/335
> sort of advertises the package handles covariates.
> However there seems to be no way to tell the merge function which
> column of the phenoData should be treated as such. Looking at the
> code, the function inSilicoMerging:::design.mat()  was clearly written
> with covariates in mind, but inSilicoMerging:::mergeCOMBAT() drops all
> columns from the original phenoData. Is this a bug or covariates are
> not supported? Or did I miss something?
> Thank you,
> Francois Lefebvre
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