Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Pairwise comparisons in DEXSeq Julien Roux Illumina/Solexa 7 07-20-2012 04:29 AM
Tophat - reporting only best hit given multi-reads/multi-maps. john_nl Bioinformatics 1 07-05-2012 01:15 PM
cuffdiif or cufflinks expr comparisons middlemale Bioinformatics 0 11-05-2010 03:44 AM
ChIP-Seq comparisons GERALD Epigenetics 2 07-09-2010 05:36 AM
Cuffdiff multi-protein vs multi-promoter RockChalkJayhawk Bioinformatics 2 03-26-2010 11:26 AM

Thread Tools
Old 12-05-2012, 10:51 AM   #1
Junior Member
Location: USA

Join Date: Dec 2012
Posts: 1
Default Multi group comparisons in baySeq

I am having trouble setting up the group model structure to test on my data(consists of 3 replicate samples for each of 4 treatments/groups).

I want to test the following models:
no differential expression(NDE)
pairwise comparisons of treatment groups for DE:
1 vs (2,3,4) 2 vs 3 2 vs 4 3 vs 4

I have completed the analysis for NDE and DE for [1 vs (2,3,4)].
Here is the replicate and model structure code I used:

Q1) If I use the following model structure as an example, what DE genes am I getting (FDR 10%)? Those that are different between groups 1,3 and 2,4, and also different between groups 2 and 4?

Q2) I need help coding the proper model structure to make pairwise comparisons where I only want to focus on two groups at a time (2 vs 3 2 vs 4 3 vs 4), replicate structure = (replicates=c(1,1,1,2,2,2,3,3,3,4,4,4))

Any suggestions would be greatly appreciated!!

LaramyE is offline   Reply With Quote

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 10:12 PM.

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