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?

Thanks in advance

Regards,
Lilach

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