Search
Question: DESeq2 combining factors in contrasts
0
gravatar for chang02_23
11 days ago by
chang02_2320
United States
chang02_2320 wrote:

I have a data set comprised of 3 conditions - a, b, and c. I want to compare DEG between group a and average of (group b + c), also just DEG between group a in b. In Limma, I would construct a design matrix like the following

design = cbind(a=c(1,1,1,0,0,0,0,0,0),
               b=c(0,0,0,1,1,1,0,0,0),
               c=c(0,0,0,0,0,0,1,1,1))
cont.matrix = makeContrasts(a-(b+c)/2, a-b, levels=design)

I'm trying to replicate my analysis with DESeq2. Here is some test data, and code to show I can extract DEG results between group a and b, b.

However, How do I get DEG between group a and average of (group b + c) ?

test_data=sapply(rep(20,9), function(x) { sample(seq(1:100), x) })
col_data = data.frame(condition=c("a","a","a","b","b","b","c","c","c"))
dds = DESeqDataSetFromMatrix(countData = test_data,
                       colData = col_data,
                       design = ~ condition)
dds <- DESeq(dds)
resultsNames(dds)
results(dds, contrast=c("condition","a","b"))

 

ADD COMMENTlink modified 11 days ago by Michael Love14k • written 11 days ago by chang02_2320
1
gravatar for Michael Love
11 days ago by
Michael Love14k
United States
Michael Love14k wrote:

Take a look at numeric contrasts described here ?results

ADD COMMENTlink written 11 days ago by Michael Love14k

Is this the correct way for comparing group a and average of (group b + c)

resultsNames(dds)
[1] "Intercept"  "conditiona" "conditionb" "conditionc"
results(dds, contrast=c(0,1,-0.5,-0.5))
ADD REPLYlink written 10 days ago by chang02_2320
1

Yes that's it.

ADD REPLYlink written 9 days ago by Michael Love14k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 116 users visited in the last hour