Saturday, December 31, 2016

noiseqbio too many false positives



###################################################
### code chunk number 33: NOISeq.Rnw:875-877
mynoiseqbio = noiseqbio(mydata, k = 0.5, norm = "n", factor="Zconditions", lc = 1, r = 20, adj = 1.5, plot = FALSE, a0per = 0.9, filter = 1,
                        # random.seed = 12345, 
                        conditions = c("control","high")
                        )#this runs 20161230 5:52pm
head(mynoiseqbio@results[[1]])
summary(mynoiseqbio@results[[1]]) #too many false positives

So, I decided that noiseqbio did not give reasonable outcomes. Although, different parameters may yield different results.

For comparison, I tried noiseq, which gave reasonable results.














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