Deseq2 - Pairwise results from 6 conditions - error non-conformable arguments
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claire • 0
@2a044aa5
Last seen 5 months ago
United Kingdom

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( )
DESeq2 • 504 views
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@mikelove
Last seen 3 days ago
United States

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

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> table(ddsM_15.5_r1$Region)

BLE LLE BJK LJK CL PEK

2 2 2 2 2 2

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I don't seem to have the same issue if I use relevel

ddsM_15.5_r1$Region <- relevel(   ddsM_15.5_r1, ref = "BLE")

I can pull out all the comparisons but I'm not sure what the difference between setting up the factors and releveling to one control is?

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