Appropriate DESeq2 design for multi-factor comparison within group?

Question

[halo22]

Hello All,

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.

Thanks!!!

Answer 1

[swbarnes2]

You don't subset the file like that. You can use different settings in the results function to return the comparison you want. Make a new column in the phenoFile that concatenates the group and concentration, and then you can do "results(dds, contrast=c("new", "A10mL", "A150,L"))