I am interested in the data analysis of ChIP-Seq data. I am interested to know how to calculate the following:
Log2 Intensity Ratios and what does it mean ? Also, the ratio is between the replicates or between a background and a replicate and how do you calculate the intensity value for each sample?
I know how the local regression (lowess) works but why is smoothing needed for ChIP-Seq data. Is it needed to remove the non-specific binding peaks ?
What does a genome-wide mean in the ChIP-Seq sample means ?
The questions are based on the Paper that was published in Nature and link of the paper is as follows: http://www.nature.com/nature/journal/v471/n7339/full/nature09725.html.
Any hints or advice will be highly appreciated.