SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
cuffdiff : time series and cummeRbund analysis apratap Bioinformatics 1 04-28-2014 03:31 AM
Cuffdiff time series bsuac6 Bioinformatics 7 11-15-2013 12:48 PM
How to analyse time-series data with edgeR ca85 RNA Sequencing 0 10-06-2011 05:04 AM
time series analysis of count data? greigite Bioinformatics 0 06-14-2011 05:11 PM
cuffdiff: time-series problem mrfox Bioinformatics 1 12-09-2010 10:08 PM

Reply
 
Thread Tools
Old 12-17-2012, 09:15 PM   #1
Jeremy
Senior Member
 
Location: Pathum Thani, Thailand

Join Date: Nov 2009
Posts: 190
Default can DESeq handle time series data now?

I notice in the latest DESeq version that it can handle GLM type experiment designs now, but the example still only does a pairwise comparison. Is it possible to do a time series using:
Code:
fit1 = fitNbinomGLMs( cdsFull, count ~ condition ) # in my case times: 0,6,12,24,48,72 hours
fit0 = fitNbinomGLMs( cdsFull, count ~ 1 )
pvalsGLM = nbinomGLMTest( fit1, fit0 )
padjGLM = p.adjust( pvalsGLM, method="BH" )
?
I got that from the DESeq reference guide but the guide doesn't actually specify what 'count ~ 1' does. I assumed it either uses condition 1 as the base or treats each sample separately instead of grouping into conditions, which does it actually do?. Is my use of it here correct?
Jeremy is offline   Reply With Quote
Reply

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 06:27 PM.


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