Dedeepya, Somehow you are getting 54 levels of "Batch". Try removing the white spaces between "Sample 1" (e.g. "Sample1"). Alternatively, use the 'sva' version of ComBat (in the biocoductor project). This will be less finicky. Thanks! Evan On Jun 3, 2013, at 7:49 PM, Dedeepya Vaka wrote: > Hello Evan, > > I am writing to you as I have trouble osting to the combat user form. I am trying to remove batch effects and know that combat performs well for this fuction, but I have troubles doing so. Here is the error message. > > > ComBat("batcheffects_samples.txt","batcheffects.txt") > Reading Sample Information File > Reading Expression Data File > Found 4 batches > Found 54 covariate(s) > Error in matrix(0, length(vec), nlevels(vec) - start + 1) : > invalid 'ncol' value (< 0) > > > Attached are my sample info file and the data file. > > Thanks, > > Diya > <batcheffects.txt><test_for_batch.txt>