soggi average plot
1
0
Entering edit mode
Wojeff • 0
@wojeff-14309
Last seen 3.7 years ago

Hi, i have several bam files from chip-seq analysis, and  i want to plot the reads coverage around gene body. How to make normalization between samples to compare them and plot them in a same picture ?

Thanks

soggi multiple bam cancer • 1.0k views
ADD COMMENT
1
Entering edit mode
kmezhoud ▴ 10
@kmezhoud-6841
Last seen 4.9 years ago
Tunisia

Hi,

You can use vsn package http://bioconductor.org/packages/release/bioc/html/vsn.html

or

Data <­-read.table("data.txt", header=T, row.name=1)

  data.std <­- apply(Data,1, function(x) x/sd(x))

or

data-z-score <-    apply(Data,1, function(x) x - mean/sd(x))

or

data_MinMax <- apply(Data,1, function(x) x - min(x) / max(x)- min(x))

or

data.logistic <- apply(Data,1, function(x) 1  /1 + 1exp(-x))

some references:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053077/

Best,

Karim

ADD COMMENT

Login before adding your answer.

Traffic: 766 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6