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Question: Discrepancy in extracting contrasts
0
gravatar for pkachroo
16 months ago by
pkachroo10
pkachroo10 wrote:

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 

 

 

ADD COMMENTlink modified 16 months ago by Michael Love22k • written 16 months ago by pkachroo10
Answer: Discrepancy in extracting contrasts
0
gravatar for Michael Love
16 months ago by
Michael Love22k
United States
Michael Love22k 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 16 months ago by Michael Love22k

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 16 months ago by pkachroo10
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