Dear all,

I'm using EDASeq to normalize my RNA-seq data.

But I'm having some trouble understanding how to normalize for gc and for
length... I got the idea that I needed to do it separately, like this:

# within and between lane normalization for GC #
dataWithinGC2 <- withinLaneNormalization(data,"gc",which="full")
dataNormGC2 <- betweenLaneNormalization(dataWithinGC,which="full")

# within and between lane normalization for length ##
dataWithinLength <- withinLaneNormalization(data,"length",which="full")
dataNormLength <- betweenLaneNormalization(dataWithinLength,which="full")

Am I thinking right? Or should I within-normalize my data for both GC and
length, like this:
dataWithin <- withinLaneNormalization(data,"length",which="full")
dataWithin <- withinLaneNormalization(dataWithin,"gc",which="full")
dataNorm   <- betweenLaneNormalization(dataWithin,which="full")

Any help is much appreciated!
C

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