Help with object class for the "Basic inference on MA gene expression" example

[moldach]

I'm wondering if it is acceptable to apply this to RNA-seq data as well?

From my note it appears that

e <- maPooling
head(pData)maPooling # row for each MA and column for each experiment

After alignment (with Bowtie for example) I generate a raw count table (row for each gene and column for each sample). Can this raw count table analyzed the same way?

If this is possible my second problem is that class(e) is:
[1] "ExpressionSet"
attr(,"package")
[1] "Biobase"

However, my raw count table class() is data.frame. How can change the class of my raw gene counts in order for the following to work:

head(pData(e))