Hello (again),

I read lots of questions on this, but can't get it to work on my own dataset. I have histone ChIP seq data for: 1) Four different tissues 2) Two treatments

I have now a normalized count of consensus peaks which I obtained as following:

#create K4 db
K4samples <- read.csv('K4samplesheet.csv')
K4 <- dba(sampleSheet=K4samples)
#count coverage for the consensus peaks
K4_count <- dba.count(K4, bUseSummarizeOverlaps=TRUE, bRemoveDuplicates = TRUE, bParallel = TRUE)
#normalize coverage to sequencing depth
K4_norm <- dba.normalize(K4_count)

I would like to create contrasts that allow me to compare for each tissue, the control vs treatment. I am not interested in the intertissue comparisons. I tried design="~Tissue+Condition+Tissue:Condition" and also reorderMeta=list(tissue,treatment) but I am not 100% sure I get the comparisons I need (I'm still learning...). If you could help me, it would be great.

Thank you

Rita