Hi,

I am using Deseq2 to do comparisons between regions of tissue.

I have set one region as the the "control" region - BLE.

I am trying to pull out the pairwise comparisons for the region named BJK which is third in the factor list. I can run results with contrast for "BLE" vs "BJK" fine but when I try to run results for "BJK" vs "PEK" I run into an error: non-conformable arguments.

All the comparisons to BLE the control region work fine but any other results I try to run have this error. Is this beacuse I have 6 samples. I have previously used contrast = to pull out A vs B, A vs C and C vs B without any problems when A was the control population.

Any help would be great, Thanks

e15.5metadata$Region <- factor(e15.5metadata$Region, 
                               levels = c("BLE","LLE", "BJK", 
                                          "LJK", "CL", "PEK")) 

> results(ddsM_15.5_r1, contrast = c("Region", "BJK", "PEK"))
Error in counts(object) %*% whichSamples : non-conformable arguments


sessionInfo( )

What is table(ddsM_15.5_r1$Region)?