I'm trying to perform a differential expression analysis using DESeq2. The dataset under study is composed by families (mostly sibling) and I wonder whether DESeq2 is suitable to analyse these data.
Can one provide relatedness information as an additional factor? If yes, how? I've noticed that DESeq2 does not support mixed model, and, thus, the family information can not be submitted as random effect (as I use to do with lme). Is it possible to estimate a within-family correlation from the data and use it for the differential analysis (as done by limma)?
The best B-plan I have is to use only one individual for each family, but this will reduce my dataset of about 1/3.
Does anyone has any suggestions?
Thanks in advance for your help,