So my coldata looks like this: sample condition 1 RDw159SIV1 A 2 RDw159SIV2 A 3 RDw159SIV3 A 4 RDw159c1 B 5 RDw159c2 B 6 RDw159c3 B 7 RDw1524SIV1 C 8 RDw1524SIV2 C 9 RDw1524SIV3 C 10 RDw1524c1 D 11 RDw1524c2 D 12 RDw1524c3 D 13 RFc169SIV1 E 14 RFc169SIV2 E 15 RFc169SIV3 E 16 RFc169c1 F
I collapsed the 3 technical replicates (A's, B's and so on). When I run resultsNames, I get the following:
resultsNames(dds) # lists the coefficients [1] "Intercept" "conditionBvsA" "conditionCvsA" "conditionDvsA" [5] "conditionEvsA" "conditionFvsA" "conditionGvsA" "conditionHvsA" [9] "conditionIvsA" "conditionJvsA" "conditionKvsA" "conditionLvsA" [13] "conditionMvsA" "conditionNvsA" "conditionOvsA" "conditionPvs_A".
Everything is being compared to A. What I want is for B to be compared to A, D to C, F to G, and so on. I 4 biological and 3 technical replicates and each biological sample is being assessed at 2 time-points. So, when I later try to use the contrast function to specify which comparisons I want, I'm limited by the options available under resultNames. How should I get around this problem? Should something be changed in the code or in the original coldata file? Thanks!
