hi Gilgi,

By incorporating batch variables into the generalized linear model, we
control for these effects, but what is happening is not a two step process
of removal and then testing.

Mike


On Sun, Jan 19, 2014 at 5:34 AM, Gilgi [guest] <guest@bioconductor.org>wrote:

>
> Hello,
>
> I have a question regarding a design, in which there is a factor for
> "batch effect". I understand how to get the p-values when taking in account
> the batch factor.
>
> I wanted to ask whether it is possible to obtain also the actual counts
> after batch effect removal.
>
> Thanks a lot,
> Gilgi
>
>  -- output of sessionInfo():
>
> none
>
> --
> Sent via the guest posting facility at bioconductor.org.
>

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