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Old 06-10-2011, 10:49 AM   #4
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Location: Research Triangle Park, NC

Join Date: Aug 2009
Posts: 245

The default is to list the data in the same gene/transcript order as the input data. The only way to get order like you wish is to sort the data yourself, by pValue, adjPvalue, fold change, whatever you wish. But the default is just to list it by input order.

Note too that if you use the two commands I wrote, you get the results back for all the genes in your input, not just significant genes. You would then have to sort that table and apply whatever statistical cutoffs you wish (e.g. sort by adjPvalue, then select only those less than 0.01).

You could do something like:

> resSig <- res[ res$padj < 0.1, ]
> head(resSig[ order(resSig$padj), ])

to see the most significant genes sorted by adjPvalue. But again, if you wrote those out to a file:

> write.table(resSig, file = "nBinom_results_lessthan_.1.txt", sep = "\t")

That file would only include those genes with an adjPvalue less than 0.1, but the table would still be sorted initially simply by the row input order of the genes. So, you would still need to sort it manually to apply whatever order you wished to see in it.
Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.
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