Hi!
I am trying to perform DEG analysis on two treatment groups using edgeR. I originally planned to keep the analysis similar to what was used for another purpose previously. To prepare the data, I used the following functions/code:
This seems to work fine, and leads to an object y with the following structure:
I planned on running the next sequence of edgeR functions as follows:
However, I receive an error upon running estimateTagwiseDisp() as follows:
I am not too confident in what I have here. Everything before estimateCommonDisp() was intended to be consistent with previous work done on this data. However, I am concerned about what we may be missing here.
Any suggestions would be greatly appreciated!
I am trying to perform DEG analysis on two treatment groups using edgeR. I originally planned to keep the analysis similar to what was used for another purpose previously. To prepare the data, I used the following functions/code:
Code:
y <- DGEList(counts=countTable, group=listGroups) keep <- rowSums(cpm(y)>1) >= 2*nRep #Filtering rows y <- y[keep, keep.lib.sizes=FALSE] #Filtering rows y <- cpm(y, TRUE, TRUE) # Option 2 (edgeR) y <- betweenLaneNormalization(y, which="full", round=FALSE)
Code:
> head(y) N.1 N.2 N.3 P.1 P.2 P.3 G1093 2.643383 2.624754 2.643383 2.800242 2.687257 2.258823 G3412 2.689673 3.302018 3.402223 4.290321 4.294549 4.354116 G4872 4.115490 4.412357 4.427337 4.526043 4.074346 4.037426 G2856 3.271944 2.946745 3.467242 2.643383 2.687257 3.043792 G3810 3.043792 3.501425 3.286707 3.547066 3.493566 3.429753 G4756 3.949146 3.653455 4.189536 4.132336 4.205552 4.074346
Code:
y = estimateCommonDisp(y) y = estimateTagwiseDisp(y) de = exactTest(y, pair=c(group1,group2)) tt = topTags(de, n=nrow(y)) nc = cpm(y, normalized.lib.sizes=TRUE)
Code:
Error in aveLogCPM.default(y, lib.size = lib.size, dispersion = dispersion) : argument "dispersion" is missing, with no default
Any suggestions would be greatly appreciated!