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Old 10-25-2011, 12:16 PM   #1
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Default ChIP-Seq Data Analysis and Normalization

I am interested in the data analysis of ChIP-Seq data. I am interested to know how to calculate the following:

1. 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?

2. 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 ?

3. 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:

Any hints or advice will be highly appreciated.

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