SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   General (http://seqanswers.com/forums/forumdisplay.php?f=16)
-   -   argument "dispersion" is missing, with no default (http://seqanswers.com/forums/showthread.php?t=72312)

SuzuBell 10-31-2016 06:08 PM

argument "dispersion" is missing, with no default
 
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:

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)

This seems to work fine, and leads to an object y with the following structure:

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

I planned on running the next sequence of edgeR functions as follows:

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)

However, I receive an error upon running estimateTagwiseDisp() as follows:

Code:

Error in aveLogCPM.default(y, lib.size = lib.size, dispersion = dispersion) :
  argument "dispersion" is missing, with no default

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!


All times are GMT -8. The time now is 01:56 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.