Question: Advice on Normalizing Baseline from NGS.Plot.R
gravatar for landrjos
15 months ago by
landrjos20 wrote:

Hi All,

I was need some advice on how to present some aggregate plot data. I have 2 categories of genes that I want to analyze. When I look at the enrichment at the TSS of these 2 gene categories for a factor from a ChIP-Seq data set I get the following result.

NGS plot peaks showing difference in base line

The plot shows Log 2 transformed input normalized (as performed by NGS.plot.r) factor read density at the TSS of gene category A and B. I would like to further normalize for the differences in the base line, to show that the genes in category B have more of the factor present relative to the surrounding baseline. How can one do this?

Alternatively, is it not legitimate to normalize out the base line. Do I need to show it as is?

chip-seq R • 447 views
ADD COMMENTlink written 15 months ago by landrjos20

Here is the link to the image.

enter image description here

ADD REPLYlink modified 15 months ago by ATpoint29k • written 15 months ago by landrjos20
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