[BioC] How does the rank product calculate the fold change

[Georg Hildebrand]

Hi,

my question is accordin to the library(RankProd) package
maybe this question is very easy, but i was not able to find an
satisfying answer.

I created a list of diff. expressed genes with the Rank product package.
Everything works well, but in the output of the topgenes() function i
do not understand how the fold change is processed.
Has anyone a hint?

It is not just the difference of the mean like in limma. Even in the
papers of breitling there is no good hint.

best regards
Georg

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fyi here is my code.
I have 3 treat. and 3 control samples for one timepoint

>cgroup = 28:30
>srgroup = 40:42
>cols = c(srgroup,cgroup) # checked
>data.rp = data.rma[,cols] #checked (log 2 expr. matrix)
#control vs treatment class
>cl = rep(c(0,1),c(3,3))#vector to classify the data1 is case 0 is
>origin = rep(1, ncol(data.rp)) #data from same origin
>gene.names = rownames(data.rp)
>RP.out <- RPadvance(data.rp, cl, origin, num.perm = 100,
		+ logged = TRUE, na.rm = FALSE, gene.names = gene.names, plot = TRUE,
		+ rand = 123)

>RP.out <- RP(data.rp, cl,  num.perm = 100,
+		logged = TRUE, na.rm = FALSE, gene.names = gene.names, plot = TRUE,
+		rand = 123)

>top.genes = topGene(RP.out, cutoff = 0.05, method = "pfp", logged = TRUE,
+		logbase = 2, gene.names = gene.names)