I am trying to use the Noiseqbio method in order to compare the results with other methods (edger, deseq2 and limma+voom).
I obtain very similar results for edger, deseq2 and limma+voom but i obtain completely different results (twices more DE genes) when i use noiseqbio.
I think i did not use the parameters of the noiseqbio function correctly. I have three replicates per conditions and i want to select the DE genes with a pvalue of 0.05 and a log fold change of 1.
my code :
mydata = NOISeq::readData(data = countsTable, factors=conditions)
myTMM = tmm(assayData(mydata)$exprs, long = 1000, lc = 0)
myfilt = filtered.data(countsTable, factor = conditions$Cellular_Type, norm = FALSE, depth = NULL, method = 1, cv.cutoff = 100, cpm = 1, p.adj = "fdr")
mynoiseq = noiseqbio(mydata, k = 0.5, norm = "tmm", factor="Cellular_Type",nclust=,conditions=c("Basal","LP"))
mynoiseq.deg = degenes(mynoiseq, q = 0.95, M = NULL)