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Question: How to use edgeR to compare multiple conditions to reference condtiion
3
gravatar for xmix
4.3 years ago by
xmix • 40
United States
xmix • 40 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, as.is=T)
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?

Thanks!
differential expression rna-seq edger • 7.6k views
ADD COMMENT • link •
modified 4.3 years ago by komal.rathi • 3.3k • written 4.3 years ago by xmix • 40
2
gravatar for Devon Ryan
4.3 years ago by
Devon Ryan ♦ 86k
Freiburg, Germany
Devon Ryan ♦ 86k wrote:
design = model.matrix(~group)
f <- glmFit(cds, design)
lrt <- glmLRT(f, coef=2:4)
topTags(lrt)

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 COMMENT • link modified 4.3 years ago • written 4.3 years ago by Devon Ryan ♦ 86k
1

I think design = ~group should be

design = model.matrix(object = ~group)

 

ADD REPLY • link written 4.3 years ago by xmix • 40

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

ADD REPLY • link modified 4.3 years ago • written 4.3 years ago by Devon Ryan ♦ 86k

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

ADD REPLY • link written 4 months ago by goodez • 420
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