SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Amplicon normalization RCJK Sample Prep / Library Generation 3 06-20-2013 05:55 AM
Data normalization dgrayson Bioinformatics 0 10-18-2012 01:59 PM
denominator for normalization shurjo RNA Sequencing 3 09-03-2012 03:35 PM
microRNA normalization kenosaki Bioinformatics 2 08-29-2011 08:15 PM

Reply
 
Thread Tools
Old 05-26-2014, 10:19 PM   #1
3sTan
Junior Member
 
Location: Germany

Join Date: May 2014
Posts: 2
Default Normalization between species

Hi all,

I am currently reading Brawand et al paper :
The evolution of gene expression levels in mammalian organs.
Can someone give me a light about the computation of their scaling factor?

"""
Specifically, among the genes with expression values in the interquartile range, we identified the 1,000 genes that have the most-conserved ranks among samples and assessed their median expression levels in each sample. We then derived scaling factors that adjust these medians to a common value. Finally, these factors were used to scale expression values of all genes in the samples.
"""

Some unclear points to me:
  • Is it a procedure similar to the DESeq scaling factor computation?
  • they have expression for different tissues in different species, are they computing the scaling factor per species (pulling the samples of the different tissues from the same specie) or pulling all the samples together?
  • what about replicates? Are they also pulled with the others or a first normalization is made between replicates?
  • in a more general way, is someone know a classical protocol to normalize samples between species?

Thanks!
3sTan is offline   Reply With Quote
Reply

Tags
inter, interspecies, normalization, scaling factor, species

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:43 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO