result does not change after relevel
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JaneDoe • 0
@a3d1cc8e
Last seen 4 days ago
Spain

Hello, Apologies if this is a basic question, but I am trying to use the relevel. But the result i.e the number of DEGs does not change before and after the relevel


dds <- DESeqDataSetFromMatrix(countData = cts,
                              colData = coldata,
                              design = ~mutant_stat+sex+age+survival)

resultsNames(dds) 
#wt_vs_mut

So, it is wildtype change when compared to mutant. Now, when i relevel such that expression change in mutant (mut) is compared to wildtype(wt)

dds$mutant=relevel(dds$mutant,ref="wt") #relevel so that the level of reference is wildtype

Now, I run deseq2 again and check if the level has been reflected

   dds <- DESeq(dds) #run again on relvelled data
   resultsNames(dds)
   #mutant_mut_vs_wt

So, yes this time it is mutant vs wildtype. But the number of DGEs does not change between the pre and post relevel. Why, is it so because i assumed that if I change the level for which comparison is happening, DEGs change.

FYI wt,n=700 mut, n=50

I may be missing something here, kindly help?

DESeq2 • 88 views
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Entering edit mode
@mikelove
Last seen 1 hour ago
United States

The only thing that you should expect to change here is the sign of the LFC.

Analogous to if you ran a t-test, then changed the order of the groups.

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