[BioC] DEXSEq warning when using TRT functions

[Simon Anders]

Hi Eva

> Here's the warning I get:
>
>> subset = fitDispersionFunction(subset)
> Warning messages:
> 1: In glmgam.fit(mm, disps[good], coef.start = coefs) :
>    Too much damping - convergence tolerance not achievable
> 2: In glmgam.fit(mm, disps[good], coef.start = coefs) :
>    Too much damping - convergence tolerance not achievable

The warning means that the dispersion fit may not describe well the 
meausred versions, and hence, you should check it. To do so, make a plot 
such as Figure 1 in the vignette.

(In the vignette, we use a function called "plotDispEst" for this 
purpose which is defined in the Sweave file. Copy and paste it from the 
DEXSeq.Rnw file -- and yes, we will move this to a more convenient place 
soon.)

Check whether the red line fits the estimated dispersions well, and 
maybe compare the plot obtained form using the old function with that 
from the new TRT functions. Maybe post the plots if you are unsure.


Also, you seem to work on a small subset of the exons:

> subset = cds.exons[1:1000,]

Subsetting is useful for testing purposes, but going down to only 1000 
exons might thin out information too much. Also, etter chose them at 
random, because often, the first items in a list of things are not 
typical. Try

subset = cds.exons[ sample.int( nrow(cds.exons), 10000 ), ]


   Simon