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Old 06-10-2011, 10:04 AM   #2
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Location: Research Triangle Park, NC

Join Date: Aug 2009
Posts: 245

The first column is just a row id taken from your input file. The data is simply presented in the same order as the input data. If you don't want to sort the data in R, just write it out to a tab delimited table and parse it in Excel (the headers will be offset by one, since that first column is not data, it's just row number relative to the input data order).

> res <- nbinomTest(cds, "Control", "Treatment")
> write.table(res, file = "nBinom_results.txt", sep = "\t")

Open nBinom_results.txt in Excel and parse it by tabs and sort it by whichever column is of interest. If set up as above, fold change will be for Treatment relative to control (ie. + is up-regulated in Treatement, and - is down-regulated in Treatment.
Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.
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