SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Help interpreting this fold change plot granger Bioinformatics 2 08-22-2016 11:30 AM
edgeR and MA-plot question moem RNA Sequencing 5 11-24-2015 10:05 PM
Interpreting a PCA plot produced with DESeq2 feralBiologist Bioinformatics 9 11-17-2015 02:24 AM
EdgeR GOF plots: interpretation of low variance seqse RNA Sequencing 0 01-29-2014 07:42 PM
edgeR: very low p-value and very high variance within the group of replicates. What's valei Bioinformatics 1 06-23-2013 11:49 PM

Reply
 
Thread Tools
Old 05-16-2017, 09:27 AM   #1
ravipatel4
Junior Member
 
Location: Ithaca, NY

Join Date: Dec 2010
Posts: 5
Default Interpreting unusual looking mean-variance plot from EdgeR

Dear all,

I am trying to find differentially expressed (DE) genes using EdgeR in a complicated experimental setting. There are two factors (each has different level of variation among replicates - the reason why the experimental setting is complicated to interpret) and each factor has a control and a treated group with two replicates for each.

I fit the GLM using a design matrix that describes my experimental setting. I get an unusual looking mean-variance plot (attached - mean-var-Plot.png). Here is my interpretation of the graph. The tagwise dispersion (light blue dots) is fit very well to the common dispersion (light blue line). However, since the raw variance (grey dots) is pretty far from the fitted tagwise dispersion, I am worried that the model might be overfitting my data and it could be bad for the analysis. Do you think this is the correct interpretation of this plot? I haven't seen this type of mean-variance plot before and therefore would like to know how would you interpret it.

Note: When I use each factor alone in the design matrix, the tagwise dispersion sits in the middle of the raw variance dots, which is how the mean-variance graphs typically look (attached - fac1.png, fac2.png).

Also, as I mentioned earlier that the level of variance (or dispersion) is different between my two factors (as the RNA levels were measured using different sequencing assays for both factors), I am wondering if EdgeR is the right method for these data, since EdgeR doesn't calculate the covariances separately for different factors.

I would highly appreciate any insights. Thanks in advance for your help.
Attached Images
File Type: png mean-var-Plot.png (56.2 KB, 4 views)
File Type: png fac1.png (57.1 KB, 2 views)
File Type: png fac2.png (57.6 KB, 1 views)
ravipatel4 is offline   Reply With Quote
Old 05-16-2017, 11:35 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,382
Default

Fore reference cross-posted: https://www.biostars.org/p/253106/
GenoMax 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 12:54 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO