In my project, we performed a RNAseq of pig embryos, whose mothers were supplemented or not with arginine on diet. We are trying to analyse the differential expression of this data using DESeq2 with a nested model: Y= mean + Sex + treatment + Sex by treatment interaction + mother within treatment + error , but it is not working, because mother should be considered as a random effect.
When we tried this model with fixed effect, the error message "Error in checkFullRank(full) : the model matrix is not full rank, so the model cannot be fit as specified. Levels or combinations of levels without any samples have resulted in column(s) of zeros in the model matrix. Please read the vignette section 'Model matrix not full rank. Vignette('DESeq2')" it is returned to us. We have followed the suggestion but we still not have success.
We have been extensively looking the DESeq2 manual, papers and forums to solve this issue, but we haven't found any similar example available. Therefore, we would like to know if it is possible to use the DESeq2 analysis with random effects?