SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to get normalized count from DESeq? xhuister Bioinformatics 17 10-19-2016 06:37 AM
NORMALIZED tetranucleotides frequency fhsantanna Metagenomics 0 09-13-2014 02:49 PM
Getting normalized counts IsBeth Bioinformatics 2 05-31-2014 10:20 AM
Normalized Values from DESeq2 TheSeqGeek Bioinformatics 5 04-11-2014 12:09 PM
Standardized vs normalized libraries vibseq Sample Prep / Library Generation 0 08-06-2009 06:17 AM

Reply
 
Thread Tools
Old 01-11-2017, 10:09 PM   #1
tedwong
Member
 
Location: Sydney

Join Date: Mar 2015
Posts: 13
Default Why should MA plot be flat after normalization?

I'm talking about the slide: http://bioinformatics.mdanderson.org...09/ma08_bw.pdf

In page 5, the title is "Why is Normalization an Issue?". The author compares the MA plot before and after normalization. He writes "Variation that is obscuring as opposed to interesting."

Q1: I can see the fitted red line before and after normalization. What's that red line?

Q2: Why is the second MA plot (after normalization) is better? The distribution is more symmetric, but what does that have anything to do with biological variation and statistical testing? Why should I care symmetry?

Last edited by tedwong; 01-11-2017 at 10:26 PM.
tedwong is offline   Reply With Quote
Old 01-12-2017, 12:44 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,476
Default

1) The expected value of the data points as a function of A.
2) We don't expect there to be a global unidirectional shift in changes, rather some genes should go up and others down.
dpryan is offline   Reply With Quote
Reply

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 05:33 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO