resultnames(dds) not giving correct output
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Entering edit mode
@mrigayamehra-12427
Last seen 7.3 years ago

Hi,

I am using DESeq2 to form a contrast between three different conditions as below:

shortname    condition
Center1    center
Center2    center
Center3    center
Edge1    edge
Edge2    edge
Edge3    edge
Swim1    swim
Swim2    swim
Swim3    swim

 

My design is as follows

coldata = with(samples,data.frame(shortname = I(shortname), condition = condition))

dds <- DESeqDataSetFromMatrix(countData = countdata, colData = coldata, design = ~ condition)

dds$condition = relevel(dds$condition, "swim")

dds <- DESeq(dds)

resultsNames(dds)

This is giving this output

[1] "Intercept"                "condition_center_vs_swim" "condition_edge_vs_swim" 

However, I want the following as output

[1] "Intercept"                "condition_center" "condition_edge"  "condition_swim" 

I want to generate contrasts on my own and then find the DE genes in my contrast.

Is there something wrong in my code. Please help...

 

 

deseq2 resultsnames • 1.3k views
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Entering edit mode
@mikelove
Last seen 3 hours ago
United States
These names are correct. You can generate contrasts on your own using the contrast argument. See ?results
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