Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
cummeRbund PCA plot glados RNA Sequencing 0 04-15-2014 02:08 PM
DESeq2 - varianace stabilized pseudocounts and PCA plot KHubbard Bioinformatics 1 11-05-2013 03:35 AM
cummeRbund MDS/PCA gene list jake13 Bioinformatics 1 08-30-2013 12:39 AM
meaning of DESeq PCA plot axis? mbk0asis Bioinformatics 4 08-27-2013 12:56 AM
Help with how to interpret density plot (cummeRbund) DonDolowy RNA Sequencing 4 07-19-2013 03:33 AM

Thread Tools
Old 04-22-2014, 04:42 AM   #1
Location: Aperture Science

Join Date: Mar 2012
Posts: 59
Default cummeRbund PCA plot

Can anyone explain cummeRbund's PCA plot?
I posted this question earleir in the RNA-sequencing forum but never got any replies so will try here in the Bioinformatics forum.

I do understand traditional PCA plots, like the one in DESeq, and cummeRbund's MDS plot, but what does everything in cummeRbund's PCA version mean? What are the dots (PCA loading factors or expression values?), and what are the arrows? (There is no explanation in the manual)
glados is offline   Reply With Quote
Old 04-22-2014, 05:45 AM   #2
Senior Member
Location: Budapest

Join Date: Mar 2010
Posts: 329

Dots are expression values transformed into PC. The arrows show how depends the given condition to the PC (you can see axes rotations.)
TiborNagy is offline   Reply With Quote

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 04:03 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO