Hi All,

I have RNA-seq data for different time points 0hr,2hr,4hr,6hrs and 8hrs.

I would like to use edgeR to get genes that are differentially expressed
throughout the experiment.
In a recent edgeR user's manual ,it has been suggested to use a dispersion
value of 0.1 in case of no replicates for organisms that are genetically
similar to humans.
so it is possible to be used for mouse data for example,what about other
organisms like yeast ??

As exact test is used to get DE genes across 2 samples and i need to get DE
genes across my time course experiment,i used GLM.

when i  used GLM model to find DE genes across my samples i ran the
following commands:

mm<-model.matrix(~0+my_groups_factor)
fit<-glmfit(my_data,mm,dispresion_value)
fit<-glmLRT(data,fit)
topTags(fit)

-----
i got:

coefficient: group8
                 logConc         logFC          PValue            FDR
gene1         .....                 .....               ....
    ....
gene2         ..                       ....
....                   ....
..
.
..


---
I have a basic question(sorry i'm not statistician)
Why the last gorup 8hrs was chooosen to be the coef.??

Thank you in advance.
Best Regards,
Rabe

	[[alternative HTML version deleted]]

