I am writing to ask for clarification as I try to use the csTest() function on my dataset. I have bulkRNAseq data from samples taken from mice for two regions (A and B), and at 6 timepoints (1,2,3,4,5,6). If I create a fitted_model with these two co-variates and also 3 cell types, is it possible to check for cell specific differentially expressed genes with one of the covariates fixed? that is to say, can I check between the two regions but only at timepoint 1? I understand that I could create a model where I only include the samples from that timepoint, but I have relatively few samples (3 per condition, 36 total) so I was hoping to fit the model to all 36 but specify a given timepoint.
I believe the answer might reside within the contrast_matrix argument, but my background level in this area of statistics and modeling is, to put it bluntly, too weak to follow what you have included in the help.
Thank you very much for your time and consideration.
Hi Ziyi Li,
I am writing to ask for clarification as I try to use the csTest() function on my dataset. I have bulkRNAseq data from samples taken from mice for two regions (A and B), and at 6 timepoints (1,2,3,4,5,6). If I create a fitted_model with these two co-variates and also 3 cell types, is it possible to check for cell specific differentially expressed genes with one of the covariates fixed? that is to say, can I check between the two regions but only at timepoint 1? I understand that I could create a model where I only include the samples from that timepoint, but I have relatively few samples (3 per condition, 36 total) so I was hoping to fit the model to all 36 but specify a given timepoint.
I believe the answer might reside within the contrast_matrix argument, but my background level in this area of statistics and modeling is, to put it bluntly, too weak to follow what you have included in the help.
Thank you very much for your time and consideration.
-ross