Hi,
Could anyone please tell me how to change the FDR from default (0.05) to 0.0001 in edgeR?
et <- exactTest(y, pair=c("1","2"))
out.adjusted <- topTags(et, n=Inf, adjust.method="BH")
out.adjusted.keep <- out$table$FDR <= 0.0001
I'm not sure if i understand this correctly, topTags function with adjust.method will adjust the pvalues from et, using BH/FDR set at 5%, which is the default. then, the FDR column of the output file are the adjusted p.values, on this case retaining only those with <=0.0001 values.
appreciate your help!
Could anyone please tell me how to change the FDR from default (0.05) to 0.0001 in edgeR?
et <- exactTest(y, pair=c("1","2"))
out.adjusted <- topTags(et, n=Inf, adjust.method="BH")
out.adjusted.keep <- out$table$FDR <= 0.0001
I'm not sure if i understand this correctly, topTags function with adjust.method will adjust the pvalues from et, using BH/FDR set at 5%, which is the default. then, the FDR column of the output file are the adjusted p.values, on this case retaining only those with <=0.0001 values.
appreciate your help!
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