Question: EdgeR User Guide: use of glmLRT vs glmQLF in oral carcinoma Case Study
0
gravatar for oakhamwolf
6 months ago by
oakhamwolf0
oakhamwolf0 wrote:

Dear all,

I'm working through the edgeR user guide and would like to understand the reasoning behind using glmLRT() over glmQFTest() to detect DE genes, specifically within the oral carcinoma Case Study (p40 onward). I see from the user guide and also edgeR glmLRT with test="F"? and other sources that for cases where the number of replicates is small, glmQFTest() is preferred for the reasons stated. However, in that particular Case Study there appears to be three biological replicates in each group, yet glmLRT() is used. Is there a reason for this? Is the choice related to the paired design (i.e. only one sample in each group within the pair) or something else? I note that in section 3.4.1 on p35 in the example covering the ideas behind paired designs, there is a similar design and glmQFTest() is used, I just can't work out why!

Any help understanding this would be very much appreciated.

Cheers

ADD COMMENTlink modified 6 months ago • written 6 months ago by oakhamwolf0
Answer: EdgeR User Guide: use of glmLRT vs glmQLF in oral carcinoma Case Study
2
gravatar for Gordon Smyth
6 months ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

The oral carcinoma case study uses glmLRT for historical reasons. The case study was written before the quasi-likelihood (QL) functions were developed. The analysis could in principle be updated to use glmQLFTest().

ADD COMMENTlink written 6 months ago by Gordon Smyth37k
Answer: EdgeR User Guide: use of glmLRT vs glmQLF in oral carcinoma Case Study
0
gravatar for oakhamwolf
6 months ago by
oakhamwolf0
oakhamwolf0 wrote:

Many thanks for the clarification and the fast response.

ADD COMMENTlink written 6 months ago by oakhamwolf0
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