Can I ask, when I run the below code:
library(qvalue) pvals <-c(0.01,0.02,0.03,0.10,0.67,0.08,0.55,0.10,0.81,0.08,0.94,0.10,0.81,0.08,0.72,0.10,0.22,0.08,0.72,0.01,0.02,0.03,0.04,0.05,0.06,0.07,0.01,0.02,0.03,0.10,0.67,0.08,0.55,0.10,0.81,0.08,0.94,0.10,0.81,0.089,0.72,0.10,0.22,0.08,0.72,0.01,0.02,0.03,0.04,0.05,0.06,0.07) qobj <-qvalue(p=pvals) pvals qobj$qvalues qobj$lfdr the qobj$qvalues list is: [1] 0.03592311 0.03592311 0.03592311 0.03991457 0.22490992 0.03991457 [7] 0.19757712 0.03991457 0.23278177 0.03991457 0.25975174 0.03991457 [13] 0.23278177 0.03991457 0.22490992 0.03991457 0.08319037 0.03991457 [19] 0.22490992 0.03592311 0.03592311 0.03592311 0.03991457 0.03991457 [25] 0.03991457 0.03991457 0.03592311 0.03592311 0.03592311 0.03991457 [31] 0.22490992 0.03991457 0.19757712 0.03991457 0.23278177 0.03991457 [37] 0.25975174 0.03991457 0.23278177 0.03991457 0.22490992 0.03991457 [43] 0.08319037 0.03991457 0.22490992 0.03592311 0.03592311 0.03592311 [49] 0.03991457 0.03991457 0.03991457 0.03991457 and the qobj$lfdr list is: [1] 0.03070397 0.04312982 0.05458114 0.13925884 0.79081046 0.11311424 [7] 0.79081046 0.13925884 0.79081046 0.11311424 0.79081046 0.13925884 [13] 0.79081046 0.11311424 0.79081046 0.13925884 0.34265237 0.11311424 [19] 0.79081046 0.03070397 0.04312982 0.05458114 0.06583569 0.07718949 [25] 0.08879583 0.10074920 0.03070397 0.04312982 0.05458114 0.13925884 [31] 0.79081046 0.11311424 0.79081046 0.13925884 0.79081046 0.11311424 [37] 0.79081046 0.13925884 0.79081046 0.12463425 0.79081046 0.13925884 [43] 0.34265237 0.11311424 0.79081046 0.03070397 0.04312982 0.05458114 [49] 0.06583569 0.07718949 0.08879583 0.10074920 Can I check that the qobj$lfdr are the FDR Q values (i.e. the number of expected false positives over the number of significant results) for each gene? Thanks [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.