[BioC] Array weights in the 'removeBatchEffect' function?

[Gordon K Smyth]

Dear Bo,

> Date: Tue, 24 Apr 2012 02:06:56 +0200
> From: bburla at botinst.uzh.ch
> To: bioconductor at r-project.org
> Subject: [BioC] Array weights in the 'removeBatchEffect' function?
>
> Dear List
>
> Is it possible to correct expression values for array weights (obtained 
> via the arrayWeights function) using the removeBatchEffect function?

No.

> Or is there any other way to obtain expression values corrected for 
> array weights,

No.  It is not theoretically possible.

In principle, one could adjust fold changes for array weights, but not 
expression values themselves.

> in order to create heatmaps or conducting clustering analyses?

In principle, plotMDS() in the limma package could take account of array 
weights, but at the moment it doesn't.

Best wishes
Gordon

> Thank you very much for your help.
> Bo
> ------------------
> B. Burla
> University of Zurich
> Zurich
> Switzerland

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