Hi,

In most of the chipseq papers, inorder to visualize the intensity signals the data is represented in the form of normalized counts. One such is this paper http://www.nature.com/nature/journal/v488/n7409/full/nature11243.html, in the supplementary methods they described the procedure as

"To generate the wig files, we extended the mapped reads to 300 bp toward the 3’ end, divided the mouse genome into 100 bp bins, and counted the number of reads that fell within each bin. We normalized the tag counts in each bin according to the total number of reads. Input reads were processed in the same way and their normalized signal intensity values were subtracted from the ChIP-Seq tracks. Therefore, the
height of each 100 bp bin in genome browser is computed as:
normalized signal intensity = normalized signal intensity(IP) - normalized signal intensity (input) "

In order to proceed with same on my own chipdata , is there any way through Bioconductor ?

any functions-

1) to divide the genome into defined windows

2) count the total number of reads

3) count the number of reads in each bin 

Check out the csaw package, if you haven't done so already. It provides methods to count reads into pre-defined windows across the genome. It's intended for differential binding analyses, but you're free to do what you want with the counts once they've been computed. There's a user's guide that you can call through csawUsersGuide(), and there's a documented workflow at https://www.bioconductor.org/help/workflows/chipseqDB.