
Similar Threads  
Thread  Thread Starter  Forum  Replies  Last Post 
Help interpreting this fold change plot  granger  Bioinformatics  2  08222016 11:30 AM 
edgeR and MAplot question  moem  RNA Sequencing  5  11242015 10:05 PM 
Interpreting a PCA plot produced with DESeq2  feralBiologist  Bioinformatics  9  11172015 02:24 AM 
EdgeR GOF plots: interpretation of low variance  seqse  RNA Sequencing  0  01292014 07:42 PM 
edgeR: very low pvalue and very high variance within the group of replicates. What's  valei  Bioinformatics  1  06232013 11:49 PM 

Thread Tools 
05162017, 09:27 AM  #1 
Junior Member
Location: Ithaca, NY Join Date: Dec 2010
Posts: 5

Interpreting unusual looking meanvariance 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 meanvariance plot (attached  meanvarPlot.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 meanvariance 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 meanvariance 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. 
05162017, 11:35 AM  #2 
Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 7,059

Fore reference crossposted: https://www.biostars.org/p/253106/

Thread Tools  

