Question: Discrepancy in extracting contrasts
gravatar for pkachroo
14 months ago by
pkachroo10 wrote:



I am trying to account for batch effect in the DESeq2 design as follows:

ddsFull<-DESeqDataSetFromMatrix(countData=countsTable, colData=colData, design=~batch+group)

My covariate of interest is "group" and has three levels 1A, 1B, 2A. I have 2 batches - A and B that need to be accounted for.

However, when I run dds<-DESeq(ddsFull) and check resultsNames(dds) it gives me: "Intercept"  "batch_B_vs_A"  "group1B_vs_1A"  "group2A_vs_1A"

A few days back when I ran the code it allowed me to correct for batch and let me extract results for the three contrasts comparing the three group (1B_vs1A, 2A_vs_1A, 2A_vs_1B). I don't understand what has changed between last time and now. 

Appreciate any help.




ADD COMMENTlink modified 14 months ago by Michael Love20k • written 14 months ago by pkachroo10
gravatar for Michael Love
14 months ago by
Michael Love20k
United States
Michael Love20k wrote:

Most likely someone upgraded the package versions. Either way, just use the ‘contrast’ argument to extract the specific contrasts you need.


ADD COMMENTlink written 14 months ago by Michael Love20k

Thanks for your quick response. You are right, despite resultsNames(dds) not showing all three contrasts, I am able to extract the results. 



ADD REPLYlink written 14 months ago by pkachroo10
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