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Question: LRT results DESeq2
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gravatar for bekah
7 months ago by
bekah20
bekah20 wrote:

Hi,

​I am running analysis on RNA Seq data using DESeq2, I have two "treatments" for each sample each with two levels

status: sham or infected
temperature: high or low.

​I have run the LRT to look at whether I am make sure I have not made any assumptions based on experimental design on whether genes are significantly dif expressed. To do this I have used the LRT

dstemp_lrt<-DESeq(dstemp, test="LRT", reduced= ~status)
res_LRT<-results(dstemp_lrt)

to give:
log2 fold change (MLE): temperature L vs H
LRT p-value: '~ status + temperature' vs '~ status'

​Am I correct in thinking that this gives the Pvalues of the genes significantly differentially expressed as a result of whether it was sham or infected in comparison to those genes sig. differentially expressed when temperature is also factored in (the interaction)?
Therefore I should also run with "reduced=~temperature" to test the same but with just temperature and then compare the two lists?


Best wishes,

​Rebekah

 

ADD COMMENTlink modified 7 months ago • written 7 months ago by bekah20

Ah cheers! So this can be used to identify if the DEG I have found when looking at the four individual experimental groups (infected L, infected H, control L, control H) can be attributed to the difference in temperature or difference in status?

 

ADD REPLYlink written 7 months ago by bekah20

Basically, yes. You should see which have the differences.

ADD REPLYlink written 7 months ago by Michael Love20k
1
gravatar for Michael Love
7 months ago by
Michael Love20k
United States
Michael Love20k wrote:

The p-value you have there tests for differences in gene expression due to temperature, accounting for differences due to status.

ADD COMMENTlink written 7 months ago by Michael Love20k
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