SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
edgeR/DESeq and multi-mapping reads Lars_R Bioinformatics 10 08-20-2013 01:25 AM
Estimating Dispersions DESeq: ALL Conditions at once, or each comparison separately? carmeyeii Bioinformatics 1 05-20-2013 01:47 AM
Specifing conditions and normaliztion in DESeq? tamari Bioinformatics 0 10-31-2012 01:04 AM
DESeq: defining conditions mouchkam Bioinformatics 2 04-10-2012 04:45 PM
Is more than two conditions possible in DESEQ? greener RNA Sequencing 5 05-09-2011 03:10 PM

Reply
 
Thread Tools
Old 03-02-2014, 12:58 PM   #1
fabou
Junior Member
 
Location: Europe

Join Date: Apr 2013
Posts: 2
Default DESeq(2): multi-conditions assay

Dear SEQanswer community

I face the following question and wonder how to approach it with DESeq or DESeq2:

I have four conditions (each with replica) A, B, C, D whereas A and B be are the controls and C and D where treated with similar but different agents. Now I'd like to identify the genes which are more pronounced differential regulated due to D than due to C.

How can I approach this? Is it advised to do it ...
  • ... pairwise and consider only genes which are significant in B vs. D but not in A vs. C (which ommits genes which are induced by both agents but with different strength)
  • ... with condition<-c(untreated, untreated, untreated, treated) and no Type and no GLM
  • ... with condition<-c(untreated, untreated, treated, treated) and Type<-('S1','S2','S1','S2') with GLM modelling count ~ Type + condition

As you might figured from the question I do not fully get what the GLM does.

Any help is highly appreciated
thank you very much in advance

fabou
fabou is offline   Reply With Quote
Old 03-02-2014, 02:02 PM   #2
mastal
Senior Member
 
Location: uk

Join Date: Mar 2009
Posts: 667
Default

Why do you have two sets of controls, what is the difference between A and B?
mastal is offline   Reply With Quote
Old 03-02-2014, 05:14 PM   #3
Michael Love
Senior Member
 
Location: Boston

Join Date: Jul 2013
Posts: 333
Default

hi Fabou,

To get at the right approach, i would also need to know what's the difference between A and B.

But if A and B are identical controls, you can compare the log2 fold change from treatment2 over treatment1 using a contrast.

If you define a condition variable with levels "control","treatment1","treatment2", and a design:

design(dds) <- ~ condition

Then you can test for genes with differential expression comparing treatment 2 vs treatment 1 using:

res2vs1 <- results(dds, contrast=c("condition","treatment2","treatment1"))

You could also combine multiple results, for example genes with low adjusted p-value from this comparison, as well as from a contrast of treatment 2 vs control, in order to define set of genes which are differentially expressed in treatment2 vs control, and vs treatment1

res2vsC <- results(dds, contrast=c("condition","treatment2","control"))

res2vs1$both <- (res2vs1$padj < 0.1 & res2vsC$padj < 0.1)
Michael Love is offline   Reply With Quote
Old 03-04-2014, 11:54 PM   #4
fabou
Junior Member
 
Location: Europe

Join Date: Apr 2013
Posts: 2
Default

Thank you Michael, I will explore the strategy you outlined.
fabou is offline   Reply With Quote
Reply

Tags
deseq, dgea, rna-seq data analysis

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:17 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO