Hi Bioconductor !

I have a time course RNAseq data from 8 time-points with 3 replicates per sample. These data were aligned with STAR, I get the featureCount output. With these file, I wan't to use MasigPro package to evaluate which genes are moving during this process. But I've got a problem with the notion of negative binomial model. I read a lot of post to understand that the RNAseq libraries follow this model due to differences between biological replicates inducing that variance differs from mean.

I've got a table with samples in columns and genes in rows, and effectively when I make a plot with log(row mean) vs log(var mean) I can see the deviation from the line mean=var.

But in this package, they said "θ must be specified and it can be computed by using available methods as edgeR" I understand that Theta is a parameter for the glm (seem to be the "shape" of the glm). But I don't know how to determine it. I read that MASS package can do this, I follow this tutoriel to better understand: https://stats.stackexchange.com/questions/10419/what-is-theta-in-a-negative-binomial-regression-fitted-with-r

but It not seem to work if i make

mean <- apply(data, 1, mean)
var <- apply(data, 1, var)
mod.NB<-glm.nb(mean~var) 
Error in glm.fitter(x = X, y = Y, w = w, etastart = eta, offset = offset,  : 
NA/NaN/Inf dans 'x'
De plus : There were 50 or more warnings (use warnings() to see the first 50)

So I switch to the edgeR notice to understand how to calculate it. I find that "In this article, we call φg the dispersion ", so It seem to be the same theta as MasigPro defines it. But I cannot find the function to calculate it ...

Does-anybody can help me to understand this problem? Maybe I miss something, I'm new in bioinformatics and statistics 

Thanks a lot nicolas

There are many tutorials on how to run the edgeR package, for example the edgeR User's Guide. If you are new to bioinformatics, that is where to start.

Finding genes that change with time is quite straightforward using a number of tools. There shouldn't be any need to do your own mathematical analysis.