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List:       bioconductor
Subject:    Re: [BioC] inSilicoMerging:::mergeCOMBAT covariates
From:       Quentin De Clerck <qdeclerc () vub ! ac ! be>
Date:       2014-04-30 15:49:00
Message-ID: 9B8DF0C6-96D3-4FFB-B0DD-38F7E758F1FF () vub ! ac ! be
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Hi Fran=E7ois,

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 yo=
u to take a look at the BatchAdjust method in the latest SCAN.UPC package.

Kind regards,

Quentin De Clerck

Le 28 avr. 2014 =E0 20:34, Fran=E7ois Lefebvre <lefebvrf@gmail.com> a =E9cr=
it :

> 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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