Question: EdgeR Warning message In estimateCommonDisp.
0
gravatar for Dr.Animo
4 days ago by
Dr.Animo10
Pakistan/Islamabad/COMSATS
Dr.Animo10 wrote:

Hi everyone, I am trying to perform DEG analysis. I've two samples each has 3 replicates (one is XR and other is YR) replicates are XR1,XR2,XR3 and YR1,YR2,YR3..

d<- DGEList(counts=as.matrix(raw.data[,2:7]), lib.size=library.sizes, group=expt)
d<- calcNormFactors(d)

At the following step, I got a warning message

d<- estimateCommonDisp(d)
Warning message:
In estimateCommonDisp.DGEList(d) :
  There is no replication, setting dispersion to NA.
d$common.dispersion
[1] NA

How to resolve this?

deg edger rna-seq R • 74 views
ADD COMMENTlink modified 4 days ago • written 4 days ago by Dr.Animo10
1

what's in ur expt variable ?? how many replicates ??

ADD REPLYlink written 4 days ago by hafiz.talhamalik230
1

(for the replicates: read the question)

ADD REPLYlink written 4 days ago by russhh4.9k
1

Does expt contain the "XR" / "YR" status, or does it encode the "XR1", "XR2", ... status. If the latter, (as I suspect) then it will be assumed that there are six separate groups, each with a single sample.

ADD REPLYlink written 4 days ago by russhh4.9k
1

Thanks for the response. I've fixed it the problem is due to expt

ADD REPLYlink written 4 days ago by Dr.Animo10

If you have these groups like XR1, XR2, XR3 you would need to indicate them like:

Name    Group
XR1 XR
XR1 XR
XR3 XR
YR1 YR
YR2 YR
YR3 YR

and then make the design as ~Group.

ADD REPLYlink written 4 days ago by ATpoint28k
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