[BioC] ComBat output header line

[Dan Tenenbaum]

Hi Lilach,

On Tue, Dec 27, 2011 at 11:39 AM, Lilach Soreq
<lilach.soreq at mail.huji.ac.il> wrote:
> Hello
>
> I have managed to run sva!
> and now I wish to know how do I specify the call for ComBat from the package
>
> in the manual it appears:
>>combat_edata = ComBat(dat=edata, batch=batch, mod=mod, numCovs=NULL,
>> par.prior=TRUE,
> (the row is cut)
>
> and I wish to enter two more variables in addition to the batch. How do I
> specify that?


I'm putting your question back on the Bioconductor list and cc'ing the
maintainer of the sva package, who can probably answer your question.

Dan


>
> Thank you!
> Happy seasons
> Lilach
>
> On Sat, Dec 24, 2011 at 8:45 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> On Sat, Dec 24, 2011 at 6:09 AM, Lilach Traivish
>> <lilachtraivish at 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 at systemsbiology.org).
>>
>> Dan
>>
>> >
>> > Thanks in advance
>> >
>> > Regards,
>> > Lilach
>> >
>> >        [[alternative HTML version deleted]]
>> >
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>
>