SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA seq data filter low count before or after normalization qliu RNA Sequencing 4 01-10-2015 01:21 AM
Different normalization methods with count data greener Bioinformatics 2 09-01-2013 05:27 AM
ChIP-Seq: A normalization strategy for comparing tag count data. Newsbot! Literature Watch 0 04-06-2012 05:00 AM
ChIP-Seq Data Analysis and Normalization snape_ar Bioinformatics 0 10-25-2011 12:16 PM

Reply
 
Thread Tools
Old 05-08-2015, 09:37 AM   #1
bjackson
Junior Member
 
Location: Denver, CO

Join Date: May 2015
Posts: 6
Default Normalization and analysis of proteomic spectral count data

I have spectral count data (SomaScan proteomics read).

What I have is protein name / uniprot identifier and a count (e.g., 188.9 or 106219.5).

I wanted to use PLGEM in R / bioconductor to analyze the data for differential expression between groups, but it says that 'normalized' data is required. Does anyone have a recommendation of what type of normalization to do?

I can't do something like dNSAF since I only have counts for called proteins, not counts for peptides.

Thanks.

Update: I've seen two thoughts on normalization, horizontal and vertical
one would be to normalize across samples (eg divide all protein counts by the total protein count for that sample so that that normalizes to the total protein load)

The other would be to normalize across each protein (e.g. mean 0, sd 1, so highly expressed proteins don't have an outsized effect on the significance levels)

You could even do the first then the second. Is there any good reason to to either or both?

Last edited by bjackson; 05-08-2015 at 01:45 PM.
bjackson is offline   Reply With Quote
Reply

Tags
normalization, proteomics, somascan, spectral counts

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 11:16 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO