Discrepancy in extracting contrasts
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pkachroo ▴ 10
@pkachroo-11576
Last seen 4.1 years ago

Hi,

 

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.

Priyanka 

 

 

deseq2 resultsnames batch effect contrast • 1.3k views
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@mikelove
Last seen 2 days ago
United States

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

 

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

 

 

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