I already got 9 .sam files from alignments from programs other than bioconductor. What can I use for getting the results about differential gene expression? All the packages use already processed data, or they already got the counts matrices so I don't know what to use for, first of all getting the count matrices, and then the differential gene expression.

Your help will be appreciated. 

Thanks

Try reading the documentation in some of the more widely used packages for DE analysis, e.g., edgeR.

biocLite("edgeR")
library(edgeR)
edgeRUsersGuide()

This focuses on how to do the DE analysis after the counts are acquired. It also provides some hints to the programs you can use to get those counts, such as the featureCounts function in the Rsubread package. If you want a full description of these earlier steps, then you can have a look at some workflows, e.g., the QL paper or Mike Love's workflow. There's a lot of documentation out there already, so take advantage of it.