I am interested in using the  Bioconductor package, "edge", for differential gene expression analysis of a timecourse dataset. Being relatively new to R, I am unclear how the data should be formatted and imported into the software. The examples provided with the 'kidney' and 'endotoxin' datasets do not clarify whether (i) the gene expression data and covariate data should be on the same or separate files, and (b) whether the gene annotation should remain as the first column in the expression data.

Here is how the kidney dataset (provided with the edge package) is constructed:

> str(kidney)
List of 3
 $ age    : num [1:72] 27 29 39 40 42 42 43 44 44 44 ...
 $ sex    : Factor w/ 2 levels "f","m": 2 2 1 1 2 2 2 1 2 2 ...
 $ kidexpr: num [1:500, 1:72] 2.74 2.68 2.73 2.73 2.77 ...

It is not clear to me if these are included in one file or in separate files.

Appreciate any help on these.

There is a vignette for this package that shows an example of how you use the kidney dataset, and I think answers your question.