Hi,
I am running a RNA-Seq analysis with edgeR. I have the results in three columns. I get the meaning of fold-change and p-value. can someone please explain to me in "simple" words, what is the meaning of the logConc? and maybe how it is being calculated??
Thanks Assa
From the edgeR user manual: logConc, the log-average concentration/abundance for each tag in the two groups being compared.
This is the log of the average abundance of the sequence read between control and experimental.
To view the calculation of the function, run the functionname without arguments and parentheses in R. For the exactTest, the relevant calculation steps for logConc are:
pair <- levels( as.factor( object$samples$group ) )[1:2]
this.pair <- (object$samples$group %in% pair)
lib.size <- object$samples$lib.size * object$samples$norm.factors
group.pair <- factor( as.vector( object$samples$group[this.pair] ) )
obj.pair <- DGEList(counts = object$counts[, this.pair], group = group.pair, lib.size = lib.size[this.pair])
q2q.pair <- equalizeLibSizes(obj.pair, disp = dispersion, null.hypothesis = TRUE)
levs.pair <- levels(group.pair)
logConc <- (log2(q2q.pair$conc$conc.group[, pair[1] == levs.pair]) +
log2(q2q.pair$conc$conc.group[, pair[2] == levs.pair]))/2
The object is of the class DGEList. Hope this helps.
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version 2.3.6
Thanks Larry, I read the manual, but I don't exactly understand, what that means. Is there a way of getting an example with numbers? I'll tell you what I have as a result. For one of my experiments I have logConc of ~-34.5, with a foldFC of 31. The read counts are for the control 71 and for the mutant 0. Can you explain to me how this is being calculated?
No, I cannot, especially with a mutant read count of 0. log(x/0) is undefined.