Entering edit mode
Hey Tibor,
It is probably a good idea to convert first. ComBat handles different
variance across batches, but if you have different variances across
samples within the same batch, then you should probably account for
this before using ComBat.
Evan
On Apr 5, 2013, at 6:00 AM, <bioconductor-request at="" r-project.org="">
<bioconductor-request at="" r-project.org=""> wrote:
> Message: 6
> Date: Thu, 4 Apr 2013 07:31:16 -0700 (PDT)
> From: "Tibor Pakozdi [guest]" <guest at="" bioconductor.org="">
> To: bioconductor at r-project.org, tibor.pakozdi at embl.de
> Cc: sva Maintainer <jleek at="" jhsph.edu="">
> Subject: [BioC] Homoscedasticity
> Message-ID: <20130404143116.8270113238B at mamba.fhcrc.org>
>
>
> Hello,
>
> Since ComBat was originally developed for microarray expression data
where homoscedasticity was assumed, do we first need to convert
heteroscedastic data such as the ones from NGS experiments into
homoscedastic (e.g. by DESeq's VST) or the method can deal with
samples of unequal variance?
>
> Thanks.
>
> -- output of sessionInfo():
>
> #
>
> --
> Sent via the guest posting facility at bioconductor.org.