SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
DESeq: GLMs for RNA-Seq with interaction terms EMeyer General 2 07-21-2014 02:10 PM
Sorting DESeq results kvk727 RNA Sequencing 0 03-18-2013 01:20 PM
Differnt results with old and new DESeq package for RNAseq biofreak Bioinformatics 5 06-09-2012 05:07 AM
Question about different results generated by DESeq. kentnf Bioinformatics 2 04-09-2012 08:14 AM
ChIP-Seq: Integrative analysis of genomic, functional and protein interaction data pr Newsbot! Literature Watch 0 11-27-2010 03:02 AM

Reply
 
Thread Tools
Old 06-27-2013, 12:31 PM   #1
ugolino
Member
 
Location: maryland, usa

Join Date: Oct 2011
Posts: 14
Default DESeq: intepreting results from interaction analysis

Hi there,

I am using DESeq to infer differential gene expression in a 2-factor design. Factor 1 (strain) and Factor 2 (condition) each have 4 levels; 3 bioreps each totaling to 48 samples. I am interesed in identifying an interaction effect between strain and condition, on gene expression:

> fit1 = fitNbinomGLMs( cdsFull, count ~ strain + condition + strain : condition )
> fit0 = fitNbinomGLMs( cdsFull, count ~ strain + condition )
> pvalsGLM = nbinomGLMTest( fit1, fit0 )
> padjGLM = p.adjust( pvalsGLM, method='BH' )
> DEresults <- transform( fit1, pval=pvalsGLM, padj=padjGLM )

Attached are results for few significant genes. I am trying to understand the fold changes and p values.
1. How do I identify which strain and which condition have a significant interaction, ie which comparison is the padj referring to? Do I need to do pairwise comparisons of each strain against each condition?

2. If the Intercept represents foldchange ratio of strain1 : condition1, are the other columns subtracted differences in fold change?

I can't seem to grasp the output, any tip is greatly appreciated.

thanks
Attached Files
File Type: txt interactionSample.txt (1.7 KB, 16 views)
ugolino is offline   Reply With Quote
Reply

Tags
deseq, interaction, rna-seq

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 08:22 AM.


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