Question: Random effects in DESeq2
0
gravatar for c.taylor
7 weeks ago by
c.taylor0
c.taylor0 wrote:

Is there any extension available/planned to the DESeq2 pipeline that would allow the inclusion of random effects in the model formula?

The dataset that I am trying to analyse includes repeat samples (at different time points) from the same individuals. However there are a large number of individuals (~200) and only a few samples per individual (total number of data points ~450). Therefore, I don’t believe that it would be advisable to fit individual as a fixed effect as it would likely lead to major overfitting. A random effect would seem perfect here and I have used it successfully in similar contexts with other simpler response variables. However as far as I am aware the standard DESeq function does not allow the inclusion of random effects. Based on other packages that fit negative binomial models, it seems that methods do exist for fitting random effects, but I don't know how to translate these to the context of DESeq.

Any suggestions much appreciated.

deseq2 • 98 views
ADD COMMENTlink modified 7 weeks ago by Michael Love25k • written 7 weeks ago by c.taylor0
Answer: Random effects in DESeq2
1
gravatar for Michael Love
7 weeks ago by
Michael Love25k
United States
Michael Love25k wrote:

This has been asked before on the support site:

https://www.google.com/search?q=site%3Asupport.bioconductor.org+DESeq2+random+effects

ADD COMMENTlink written 7 weeks ago by Michael Love25k

Thanks very much for your help! I had tried using the search function within the bioconductor site, but for some reason that didn't turn up the linked question.

https://support.bioconductor.org/local/search/page/?q=deseq2+random

only gives this page and an unrelated question

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by c.taylor0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 147 users visited in the last hour