Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
what is a read group? wenhuang Bioinformatics 4 04-03-2014 05:46 AM
DESeq - High Count Variablity across Samples dav1dmartin Bioinformatics 4 12-06-2012 08:23 AM
DESeq Estimate Dispersion mattia Bioinformatics 1 02-09-2012 01:42 AM
BWA:high amount of unique alignments despite high mismatch tolerance moritzhess Bioinformatics 2 09-05-2011 11:31 AM
Read Group comorado Bioinformatics 3 05-06-2010 08:36 AM

Thread Tools
Old 07-16-2012, 03:54 PM   #1
Location: Southwest

Join Date: Oct 2009
Posts: 19
Default DESeq high within group dispersion

Hi forum,

I am analyzing counts data from Tophat bam followed by HTSeq.
I have 11 biological replicates for group 1 and 10 biological replicates for group 2.

Looking at the attached dispersion plots, is it a fair interpretation that there
is too much within group dispersion (most values around 1) and within group dispersion is simply too large for anything called differentially expressed? I found ~150 genes with p<0.05 and none of the survived 0.1 FDR (giving padj=1 for all).

What'd would be a suggested way to analyze this data further?


Attached Images
File Type: png MA.png (6.0 KB, 32 views)
File Type: png case_1.png (24.1 KB, 37 views)
File Type: png case_2.png (24.2 KB, 25 views)

Last edited by wdt; 07-16-2012 at 04:28 PM. Reason: typo correction
wdt is offline   Reply With Quote

deseq, dispersion

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 02:28 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO