Thank you.
Yes, this was the case (I am new with R), so I was unaware of the
implementation in sva.

Lilach

On Sat, Dec 24, 2011 at 8:45 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

> On Sat, Dec 24, 2011 at 6:09 AM, Lilach Traivish
> <lilachtraivish@gmail.com> wrote:
> > Dear list members,
> >
> > I applied ComBat to control for batch effect in Affymetrix microarray
> data.
> >
> > I managed to get results from ComBat only when adding the skip parameter
> as
> > follows:
> > ComBat('exp_data.txt','sample_information_file.txt',skip=1);
> >
> > However, the header row of the results file misses one value - at the end
> > of the header row.
> > The missing sample same is actually of the first sample which is present
> in
> > the sample information file. Thus, I assume that all the sample names are
> > given in an offset of 1. Is is possible that this is the case? As I wish
> to
> > use the output of ComBat as an input for differential expression
> analysis,
> > how can this issue be resolved?
>
> It looks like you are not asking about the ComBat method in the sva
> package, but instead a script that is not a part of Bioconductor.
>
> You should probably contact the maintainer of that script
> (cplaisier@systemsbiology.org).
>
> Dan
>
> >
> > Thanks in advance
> >
> > Regards,
> > Lilach
> >
> >        [[alternative HTML version deleted]]
> >
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>

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