Dear R. stark,
Following your answer, these are my steps :
k4dba <- dba(sampleSheet = chipk4)
k4count <- dba.count(k4dba,bParallel = T)
k4norm <- dba.normalize(k4count)
k4model <- dba.contrast(k4norm,design="~Tissue+Condition+Tissue:Condition",bGetCoefficients = T)
The coefficient obtained are:
"Intercept" "Tissue_C_vs_A" "Tissue_B_vs_A"
"Condition_3_vs_1" "Condition_2_vs_1" "TissueC.Condition3"
"TissueB.Condition3" "TissueC.Condition2" "TissueB.Condition2"
Currently when I want to make a contrast on DESeq2 for example:
What is the difference between Tissue C and B ? -->
contrast = list( "Tissue_C_vs_A" "Tissue_B_vs_A" )
Or if I want the interaction i.e, the condition 2 on the tissue B -->
contrast = c("TissueB.Condition2")
For DiffBind, how to make these contrasts ? Using the
dba.report() and before the
Moreover, using a simply
relevel() can I modify the reference level of the Tissue or Condition ?