soggi average plot
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Wojeff • 0
@wojeff-14309
Last seen 15 months 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 • 472 views
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kmezhoud ▴ 10
@kmezhoud-6841
Last seen 2.5 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

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