Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
2
0
Entering edit mode
@simarsidhu25-12016
Last seen 5.4 years ago

I want to determine DGE analysis with my data that don't have any replicate. I just want to know that can I use glmQLFit and then glmLRT as I am not getting any DE genes by glmFit? 

edger differential gene expression glmlrt() • 1.9k views
ADD COMMENT
0
Entering edit mode

But, the exact test is only applicable to experiments with a single factor and I have more than one factor.

ADD REPLY
0
Entering edit mode

Well, in that case, you can use glmFit() and glmLRT(), can you not?

ADD REPLY
0
Entering edit mode

Yes, but I am getting single DE gene. But I am getting good results when I am using glmQLFit() and glmLRT(). Would it be possible?

ADD REPLY
0
Entering edit mode

No it is not possible. I don't know what you are doing (you don't give code) but it cannot be correct.

It isn't even possible to run glmQLFit() if you don't have replicates -- it will return an error.

ADD REPLY
0
Entering edit mode

Thanks, I have got the point.

ADD REPLY
4
Entering edit mode
@gordon-smyth
Last seen 2 hours ago
WEHI, Melbourne, Australia

You cannot use glmQLFit() if you don't have replicates.

In the absence of replicates, the only choices are exactTest() or glmFit() followed by glmLRT().

In the absence of replicates, you have to set the dispersion yourself. If you don't have any DE genes and you think you should, then apparently you have set the dispersion too high. This has nothing to do with trying to change the edgeR functions you are using.

ADD COMMENT
0
Entering edit mode
@ryan-c-thompson-5618
Last seen 23 months ago
Scripps Research, La Jolla, CA

glmQLFit/glmQLFTest can be used almost anywhere that glmFit/glmLRT can, but it's not going to give you a longer list of significant genes than glmFit/glmLRT. In fact, it's almost certain to do the opposite.

Performing a differential expression test with no replicates is a last resort method, and you should not be surprised when it gives you no significant results.

ADD COMMENT

Login before adding your answer.

Traffic: 402 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6