SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Rscript plot for y-axis kushald Bioinformatics 1 05-15-2013 09:19 PM
DESeq vsd vs log plot problem phred Bioinformatics 0 03-23-2013 07:23 AM
DESeq-strange disoersion plot and using shorth tellsparck Bioinformatics 10 02-02-2013 10:49 AM
DESeq Plot Error coralgirl Bioinformatics 2 11-29-2011 10:35 AM
DESeq Output Plot and Options silverlining Bioinformatics 3 09-20-2011 12:48 AM

Reply
 
Thread Tools
Old 08-20-2013, 07:52 PM   #1
mbk0asis
Member
 
Location: Korea

Join Date: Dec 2011
Posts: 41
Default meaning of DESeq PCA plot axis?

What does DESeq PCA plot axis mean?

If one sample has higher x- or y-value than others in the plot, does that mean it's better or worse than other?

Can someone explain to me?
mbk0asis is offline   Reply With Quote
Old 08-20-2013, 11:42 PM   #2
Simon Anders
Senior Member
 
Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994
Default

When interpreting a PCA plot, your only supposed to look at the distances between points, which tell you how similar the represented objects (here: samples) are. In DESeq, the point is that it allows you to check whether your replicates are really more similar to each other than to the other samples.

PCA is nothing specific to DESeq but a general concept that is used very frequently in exploratory statistics, and hence useful to know about.

For a very easily understandable introduction, see the following book. Just looking through chapter 1 will give you an idea:

Michael Greenacre: Biplots in Practice (Fundación BBVA, 2010), available on-line here

Last edited by Simon Anders; 08-20-2013 at 11:47 PM.
Simon Anders is offline   Reply With Quote
Old 08-21-2013, 12:21 AM   #3
mbk0asis
Member
 
Location: Korea

Join Date: Dec 2011
Posts: 41
Default

So I can just ignore numbers on the axis in this case...

Thank you for quick reply and your great software!!!
mbk0asis is offline   Reply With Quote
Old 08-26-2013, 12:52 AM   #4
mbk0asis
Member
 
Location: Korea

Join Date: Dec 2011
Posts: 41
Default

One more question, can you make the plot to show the spots' names?
mbk0asis is offline   Reply With Quote
Old 08-27-2013, 12:56 AM   #5
Wolfgang Huber
Senior Member
 
Location: Heidelberg, Germany

Join Date: Aug 2009
Posts: 109
Default

Dear mbk0asis
this is really an R question, nothing specific to DESeq. At the most basic level, have a look at the functions text, identify and locate in R's default graphics package. Then, and there are many more options - just try a web search for 'interactive scatterplots in R'.
__________________
Wolfgang Huber
EMBL
Wolfgang Huber is offline   Reply With Quote
Reply

Tags
deseq, pca plot

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 09:09 AM.


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