I am trying to run DE analysis using DESeq2 and wanted to know what would be a better/correct design matrix for my analysis. I have two disease condition A and B. Cells(CD4) from patient groups A and B were treated with different concentration of a certain chemical. The concentrations are 10ml, 50ml, 100ml, 150ml and 200ml. We would like to make the following comparisons for groups A and B separately.
10ml vs 150ml 50ml vs 150ml 100ml vs 150ml 10ml vs 200ml 50ml vs 200ml 100ml vs 200ml Sample phenoFile: Groups Sample Concentration A Well1 10ml A Well2 50ml A Well3 100ml A Well4 150ml . . . B Well20 10ml B Well21 50ml B Well23 100ml B Well24 150ml
Considering the fact that we are interested in performing comparisons within the groups and not between groups A and B, I was considering splitting the pheno file into two by groups. Then further subset the pheno file by comparison combinations like 10ml and 150ml, 50ml and 150ml, 100ml and 150 etc and then use design as design=~concentration. Is there a better method to do all the comparisons instead of subsetting the pheno file by concentrations? I really don't mind subsetting by groups but the other subsetting seems too much and there should be a better way to do this. Hope the question is clear. I appreciate all your inputs.