Hello all, I have got some RNAseq results back from a group of patients and a group of controls. I ran DESeq2 to see which genes where significantly differential expressed. When I looked at the PCA plots generated in the DESeq2 on galaxy it didn't group perfectly and I was wondering if it is possible to include Co-Variants like ages ect in the analysis? any ideas???
For covariant analysis in Deseq2, multiple top-level factors can be specified and populated with sub-factor levels and counts.
One top-level factor containing two sub-factor levels: https://galaxyproject.org/tutorials/nt_rnaseq/#perform-differential-gene-expression-testing
Two top-level factors each containing two sub-factor levels: https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html#analysis-of-the-differential-gene-expression
Hope that helps! Jen, Galaxy team