Question: Advice on Normalizing Baseline from NGS.Plot.R
0
gravatar for landrjos
15 months ago by
landrjos20
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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1597 users visited in the last hour