Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
CummeRbund (csVolcano plot) question prios RNA Sequencing 5 07-01-2013 04:22 PM
R: heatmap color palette akolman Bioinformatics 5 06-16-2011 12:51 PM
Bowtie and Color Space cutcopy11 SOLiD 9 02-05-2010 03:50 AM
Bowtie -Color spaces anusha Bioinformatics 7 02-03-2010 06:05 AM
direct mapping of color-space data against color-space begsch SOLiD 1 09-09-2009 10:25 PM

Thread Tools
Old 07-15-2013, 06:00 PM   #1
Senior Member
Location: NC State, Raleigh, NC

Join Date: Mar 2013
Posts: 107
Default Missing 'Yes' and Color in my CummeRbund csVolcano

Hello SeqAnswers community,

Does anyone know why my csVolcano plot is not showing 'Yes' under significant in the legend?

When I try the following, there is no change:
> png(file="csVolcano.png")
> csVolcano(genes(cuff_data_1),'S1','S2', showSignificant=TRUE)

Yes, I am aware there is a cluster around y-axis value 4. From what I can tell, this is due to a minimum limit in p-value (0.0001) that's a default in CuffDiff. Loyal's trick (below) on didn't change the cluster problem.

v+ scale_y_continuous(limits = c(0, 20))

I'd appreciate any help.

Thanks and God bless,

jmwhitha is offline   Reply With Quote
Old 07-18-2013, 07:23 AM   #2
Senior Member
Location: NC State, Raleigh, NC

Join Date: Mar 2013
Posts: 107
Default Actually figured this out!

Hello all,

I figured this one out. You need the alpha and showSignificant=T paramaters in the command.

csVolcano(genes(cuff_data_1),'S1','S2', alpha=0.05, showSignificant=T)

jmwhitha is offline   Reply With Quote

cuffdiff, cummerbund, loyal, showsignificant, volcano

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 12:06 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO