Entering edit mode
Catarina Almeida
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30
@catarina-almeida-6053
Last seen 10.0 years ago
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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