[BioC] ComBat output header line

[Dan Tenenbaum]

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]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor