SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
DEXSeq - more than two different conditions yylilly RNA Sequencing 22 04-25-2019 09:00 PM
DESeq2 (Mutant/WT + Two Conditions) TheSeqGeek Bioinformatics 6 05-06-2014 06:04 PM
Looking for replicated conditions IsBeth Bioinformatics 3 03-26-2014 05:44 AM
DESeq2: Difference between condition+type vs. 3 conditions mevers Bioinformatics 3 09-02-2013 02:17 AM
Is more than two conditions possible in DESEQ? greener RNA Sequencing 5 05-09-2011 04:10 PM

Reply
 
Thread Tools
Old 01-21-2015, 04:39 PM   #1
mattanswers
Member
 
Location: Boston

Join Date: Oct 2009
Posts: 65
Default 4 conditions in DESeq2

I have four conditions A, B, C, and D that each have three HTSeq count files.

I want to use DESeq2 to compare A to B, A to C, A to D, B to C, B to D etc.

With DESeq, I would bring all the 12 files into a countDataSet and then I could specify which of the conditions to compare.

With DESeq2, I can bring all the 12 files into a DESeqDataSet, but I can not figure out how to do specify the particular comparisons.
mattanswers is offline   Reply With Quote
Old 01-21-2015, 08:00 PM   #2
Dario1984
Senior Member
 
Location: Sydney, Australia

Join Date: Jun 2011
Posts: 166
Default

It's easy. Use the contrast variable of the results function. Comparing all pairs of contrasts is not a good idea, though. Why don't you have a better biological hypothesis ?
Dario1984 is offline   Reply With Quote
Old 01-21-2015, 08:08 PM   #3
mattanswers
Member
 
Location: Boston

Join Date: Oct 2009
Posts: 65
Default

We have wild type condition A and wild type condition B as well as treated condition A and treated condition B. So, we would like to see changes in gene expression between condition A and condition B, as well as changes in gene expression between wild type and treated.

Will contrast provide us with this ? To me it seems like the analysis is done by the DESeq function and the results function just organizes the output of the DESeq function.
mattanswers is offline   Reply With Quote
Old 01-22-2015, 12:45 AM   #4
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

Yes, a contrast allows you to perform pretty much any comparison you want. Note that the comparisons to A don't require contrasts, since those are just fit coefficients.
dpryan is offline   Reply With Quote
Old 01-22-2015, 07:03 AM   #5
Michael Love
Senior Member
 
Location: Boston

Join Date: Jul 2013
Posts: 333
Default

hi Matt,

For lots more information about what you want to do, check out the man page for ?results and section 3.2 Contrasts in: vignette("DESeq2")
Michael Love is offline   Reply With Quote
Old 01-22-2015, 12:06 PM   #6
mattanswers
Member
 
Location: Boston

Join Date: Oct 2009
Posts: 65
Default

Thank you very much for your answers Dario, Devon and Michael !
mattanswers is offline   Reply With Quote
Old 01-22-2015, 12:11 PM   #7
Michael Love
Senior Member
 
Location: Boston

Join Date: Jul 2013
Posts: 333
Default

> "Note that the comparisons to A don't require contrasts, since those are just fit coefficients."

Safest always to use contrast=c("condition","B","A"), because when we have expanded model matrices for symmetric shrinkage, then the coefficients are not B_vs_A, but simply A, B, etc. This will be clear from resultsNames(dds)

Last edited by Michael Love; 01-22-2015 at 12:24 PM.
Michael Love is offline   Reply With Quote
Old 01-22-2015, 12:15 PM   #8
mattanswers
Member
 
Location: Boston

Join Date: Oct 2009
Posts: 65
Default

OK. Thank you for clarifying that.
(And also for making DESeq2 !)
mattanswers is offline   Reply With Quote
Reply

Tags
deseq2

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 08:53 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO