[BioC] visualise model fit in edgeR

[Gordon K Smyth]

Hi Iain,

You're asking a hard question, as drawing nice tutorial pictures for any 
statistical method can be lots of work, and the context here is harder 
than most.  I think I'd find it hard to think of a good picture like you 
describe, even if I was just doing a ordinary multiple regression using 
lm() with univariate normal data.  What covariate or factor are you 
testing for?  Can you describe the picture you would draw if this was just 
an ordinary multiple regression problem?

Best wishes
Gordon

------------- original message ----------------

[BioC] visualise model fit in edgeR
Iain Gallagher iaingallagher at btopenworld.com
Tue Oct 25 16:06:11 CEST 2011


Dear List

I have been using the glmFit method in edgeR to analyse some RNA-Seq data. 
I will soon be presenting this data to a more statistically naive audience 
(and I'm no expert myself) and I was hoping to be able to prepapre a 
figure demonstrating how this particular edgeR analysis approach works.


Basically what I'd like to do would be to plot count data for one (ore 
perhaps a few) of my genes and then draw a couple of lines showing the fit 
of the null and alternative models used in the glmLRT method of edgeR to 
assess gene regulation between conditions.


I was hoping that this would allow me to illustrate the concept of testing 
for the likelihood of model fit and hence gene regulation between 
conditions.

If anyone could help I'd be grateful.


Best

Iain

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