How do you recommend correcting for covariates then? I am currently running CellPhoneDB separately on 3 non-overlapping subsets of data corresponding to 3 different conditions and then comparing the results to infer differences in underlying immune cell responses. I later observed that atleast 2 clinical covariates are significantly associated (p-value<0.005) with these 3 different conditions. How would I be able to tell if the difference(s) in immune cell interactions between these 3 conditions is not due to differences in these 2 clinical covariates? Any suggestions appreciated!
(Happy to open this as a separate question :))
Hi @mief ,
How do you recommend correcting for covariates then? I am currently running CellPhoneDB separately on 3 non-overlapping subsets of data corresponding to 3 different conditions and then comparing the results to infer differences in underlying immune cell responses. I later observed that atleast 2 clinical covariates are significantly associated (p-value<0.005) with these 3 different conditions. How would I be able to tell if the difference(s) in immune cell interactions between these 3 conditions is not due to differences in these 2 clinical covariates? Any suggestions appreciated! (Happy to open this as a separate question :))
Many thanks in advance,
Best, Manik
Originally posted by @Manikgarg in https://github.com/Teichlab/cellphonedb/issues/145#issuecomment-877671926