SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNAseq time course data rmberka RNA Sequencing 7 12-16-2013 07:03 AM
Comparative Time Series Analysis of RNA-Seq data? ashuchawla Bioinformatics 8 07-25-2013 12:12 PM
can DESeq handle time series data now? Jeremy RNA Sequencing 0 12-17-2012 09:15 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

Reply
 
Thread Tools
Old 08-07-2013, 05:32 AM   #1
Mocca
Junior Member
 
Location: Oslo

Join Date: Mar 2012
Posts: 9
Post RNAseq time series data w/ controls for each time point

Hi everyone,

I am currently working on a RNAseq data set consisting of 4 time points where each time point has 6 challenged and 6 control individuals (not paired). I have used both DEseq and edgeR for pairwise comparisons such as: time 1 - challenged vs control which worked nicely.

I am not sure that the reported DE genes at one time point is comparable to the DE genes at another time point. Thus I am looking for a package that can handle time series data. I have found several but none of them handles controls on each time point but prefers a base line expression level or a time 0 (which I don't have).

I can manage with my pairwise analyses, but if any of you have good suggestions to what I might try I would appreciate it greatly!

Thanks in advance
Mocca is offline   Reply With Quote
Old 08-07-2013, 05:53 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

You could use DESeq or edgeR still and just not do the pair-wise comparisons. Using DESeq syntax:
Code:
fit1 <- fitNbinomGLMs(cds, count~treatment*time)
fit0 <- fitNbinomGLMs(cds, count~time + treatment:time)
pvals <- nbinomGLMTest(fit1, fit0)
...assuming you're interested in genes that are differentially expressed by treatment when accounting for time point and a possible time-point:treatment interaction.
dpryan is offline   Reply With Quote
Old 08-07-2013, 11:12 PM   #3
Mocca
Junior Member
 
Location: Oslo

Join Date: Mar 2012
Posts: 9
Default

Thanks for the reply.

I didn't consider doing it this way. Got a bit caught up in my control samples i guess. Will give it a try!

Cheers
Mocca is offline   Reply With Quote
Reply

Tags
deseq, edger, illumina, rnaseq, time-series

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 02:24 AM.


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