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Question: edgeR 4 conditions
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gravatar for Paolo Kunderfranco
4 months ago by
Paolo Kunderfranco350 wrote:

Dear All,

I am new to multifactor analysis with edgeR, I have the following 12 samples (4 conditions and 3 replictaes)

sample type diet
sample1 wt no
sample2 wt no
sample3 wt no
sample4 ko no
sample5 ko no
sample6 ko no
sample7 wt yes
sample8 wt yes
sample9 wt yes
sample10 ko yes
sample11 ko yes
sample12 ko yes

 

I would like to find genes with these properties:

- genes differentially modulated between wt-no_diet group (sample1-3) and ko-no_diet group (sample4-6) 

- genes that are affected by the diet treatment only in ko group

- genes whose expression in the ko-yes_diet group (sample10-12) tends to get similar to the expression in the wt-no_diet group (sample1-3).

 

Any suggestion will be greatly appreciated, 

Best

Paolo

 

ADD COMMENTlink modified 4 months ago • written 4 months ago by Paolo Kunderfranco350
1
gravatar for Aaron Lun
4 months ago by
Aaron Lun16k
Cambridge, United Kingdom
Aaron Lun16k wrote:

You have... four samples, with three technical replicates of each? Or four groups, with three biological replicates in each? Your question title says "diet", but I don't see any mention of this factor in the post.

In any case, you should read the edgeR user's guide if you want to know how to use edgeR.

P.S. If the sample description is meant to be in a table, you should format it appropriately.

ADD COMMENTlink modified 4 months ago • written 4 months ago by Aaron Lun16k

Dear Aaron,

I formatted the table as requested, now it should be much more readable. I read in the user-guide but I find it difficult to create this multi-factor analysis,

Best

Paolo

 

ADD REPLYlink written 4 months ago by Paolo Kunderfranco350

Read chapter 3, and section 3.3.1 in particular. Just combine the two factors into a single factor and set up the design matrix with four groups, i.e., one group for each combination of diet and genotype.

ADD REPLYlink modified 4 months ago • written 4 months ago by Aaron Lun16k
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