Question: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
0
gravatar for simarsidhu25
2.9 years ago by
simarsidhu250 wrote:

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? 

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by simarsidhu250

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

ADD REPLYlink written 2.9 years ago by simarsidhu250

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

ADD REPLYlink written 2.9 years ago by Gordon Smyth39k

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 REPLYlink modified 2.9 years ago by Gordon Smyth39k • written 2.9 years ago by simarsidhu250

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 REPLYlink modified 2.9 years ago • written 2.9 years ago by Gordon Smyth39k

Thanks, I have got the point.

ADD REPLYlink modified 2.8 years ago • written 2.9 years ago by simarsidhu250
Answer: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
2
gravatar for Gordon Smyth
2.9 years ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:

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 COMMENTlink modified 2.9 years ago • written 2.9 years ago by Gordon Smyth39k
Answer: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
0
gravatar for Ryan C. Thompson
2.9 years ago by
The Scripps Research Institute, La Jolla, CA
Ryan C. Thompson7.4k wrote:

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 COMMENTlink modified 2.9 years ago • written 2.9 years ago by Ryan C. Thompson7.4k
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