Hello, I am doing a temporal analysis of my RNA seq data:

NBp <- p.vector(matrix_counts, design, counts=TRUE)

NBt <- T.fit(NBp)

names(NBt)

get<-get.siggenes(NBt, vars="groups")

s<-get$summary

"s" is a dataframe which contains the significant genes for each comparison, each experimental group vs. the control group. 

I got around 6000 genes for each comparison but I need to select the most important or significant ones. Are the results in descendent order of significance? Can I select for example the 30 first rows (genes)? or how many should I select? If they are not in a particular order, what should I do to get a loweramount of genes?

Thank you,

Pilar.

Looking at the code for get.siggenes, it doesn't appear that there is any ordering done to the matrix. Sorting and selecting data from a matrix are very simple things to do in R, and there is a document intended to cover such things that you could read.