Deseq2 multiple comarison

Question

[1769mkc]

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

[BioinfGuru]

You'll get more support on bioconductor for this question.

Answer 1

[Carlo Yague]

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.

Answer 2

[Devon Ryan]

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.

[1769mkc]

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

[1769mkc]

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

[Devon Ryan]

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.