Question: How to use edgeR to compare multiple conditions to reference condtiion
gravatar for xmix
4.5 years ago by
United States
xmix40 wrote:

I have an RNA-seq experiments with a control, and 4 treatments, for each I have 3 replicates. I would like to find genes that are differentially expressed in any of these conditions compared to the control samples.

Meaning if gene A is up/down-regulated in one or more of the treatments compared to the control, I would like to know about it.

lcd = read.delim('mydata', row.names=1,
group = factor(c(rep("ctrl", 3), rep("treat1",3), rep("treat2",3), rep("treat3",3),rep("treat4",3)))
cds  <- DGEList(lcd, group = group)

 What is the alternative for using exactTest multiple times and intersecting the results, given that I would not like to average the expression of the treatments as the different treatment have different consequences?


ADD COMMENTlink modified 4.5 years ago by komal.rathi3.4k • written 4.5 years ago by xmix40
gravatar for Devon Ryan
4.5 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:
design = model.matrix(~group)
f <- glmFit(cds, design)
lrt <- glmLRT(f, coef=2:4)

In other words, you'd test the full model against one lacking group information.

Edit: BTW, you might find this older thread from the bioconductor list useful. It's often best to search that list when a question arises, since odds are good someone has asked a similar question there (or here) before.

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Devon Ryan88k

I think design = ~group should be

design = model.matrix(object = ~group)


ADD REPLYlink written 4.5 years ago by xmix40

You are correct! Good catch. I've updated the answer to correct that mistake.

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by Devon Ryan88k

I know this is old, but why isn't it coef=2:5??

ADD REPLYlink written 6 months ago by goodez460
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