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Deseq2 multiple comarison

I m using deseq2 for my samples such as Wild type[untreated] , and two treated condition [with vitamin D] and Retinoic acid

and my samples are in replicates ,I want to compare the differential expression between WT vs treated[Vitamin D] and WT vs Retinoic acid .so here is my code im using but Im not sure if its doing what i want to do..

condition <- factor(c(rep("WT", 2), rep("AT", 2),rep("VD",2))))`


(coldata <- data.frame(row.names=colnames(countdata), condition))`
dds <- DESeqDataSetFromMatrix(countData=countdata, colData=coldata, design=~condition)
dds

Any suggestion or help would be highly appreciated

rna-seq r
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updated by Devon Ryan Devon Ryan • written by 1769mkc 1769mkc

2 answers

Looks good to me. From the dds table, you will just need to extract the contrasts now (VD vs wt and AT vs WT) using the results() function documented here.

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written by Carlo Yague Carlo Yague

Given your design, you'll want to ensure that WT is the base level for comparisons, which it's currently not.

condition <- factor(c(rep("WT", 2), rep("AT", 2),rep("VD",2))), levels=c("WT", "AT", "VD"))

Now when you use results() the coefficients (2 will be AT vs. WT and 3 will be VD vs WT) will be the comparisons you want.

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written by Devon Ryan Devon Ryan

okay let me try this and i will let you know..

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written by 1769mkc 1769mkc

can you explain me "(2 will be AT vs. WT and 3 will be VD vs WT" why?

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written by 1769mkc 1769mkc

This requires knowing how the model matrix will end up getting made. R will create the intercept from the base level of the factor, so all comparisons will be versus it. The other coefficients will be ordered according to the factor levels.

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written by Devon Ryan Devon Ryan

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