[BioC] inSilicoMerging:::mergeCOMBAT covariates

François Lefebvre lefebvrf at gmail.com
Mon Apr 28 20:34:00 CEST 2014


I was testing the package inSilicoMerging, particularly to perform the
COMBAT batch effect removal.

The original paper


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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