I'm a student and a beginer with R tool for RNA-seq analysis.
I've some Fastq files that I want to (i) convert into BAM file using LIMMA package in R and (ii) make an alignment with genome reference using Toophat tool.
The probleme is that, after reading the LIMMA userguide, I didn't catch what scripts use for those preliminary analysis.
limma isn't designed to convert FASTQ files into BAM files. After reading (?) the limma User's Guide, I am mystified as to why you would think that it is intended for that purpose. Can you say why you think that?
TopHat isn't a Bioconductor tool, and this is a forum to help people use Bioconductor tools only. You could post your question about TopHat on Biostars.org, or better yet just read the TopHat manual. You will get much farther by doing your own learning rather than simply trying to get others to write a tutorial for you.