SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
What is the meaning density in CummeRbund plots? Carlos Borroto Bioinformatics 16 12-29-2016 10:05 PM
volcano plots cummeRbund godzilla07 Bioinformatics 8 02-04-2015 01:55 PM
CummeRbund scatter plots of two replicates HiFl Bioinformatics 0 10-01-2014 11:07 AM
Fruit Fly CummeRbund Plots Are Not The Same jmwhitha Bioinformatics 10 09-26-2014 10:10 AM
CummeRbund plots godzilla07 Bioinformatics 1 08-10-2012 05:00 AM

Reply
 
Thread Tools
Old 07-24-2015, 06:20 AM   #1
rumeys
Junior Member
 
Location: AA

Join Date: Jul 2015
Posts: 3
Default CummeRbund plots come out in a different way than they are in the Nature protocol

Hi everyone,
I am trying to complete the procedure in the Nature Protocol Paper (Differential gene and transcript expression analysis of RNA-seq experiments with Tophat and Cufflinks, by Trapnell et al.)

The thing is that my CummeRbund plots are not similar with those in the paper. For example, the attached density plot is very different than expected. You may observe the graphs(density, scatter and volcano) in the attached pdf of the following post.

What can I do now? Does anyone have a suggestion?

The R commands are written as in the protocol.
cuff_data <- readCufflinks('diff_out')
csDensity(genes(cuff_data))
csScatter(genes(cuff_data), 'C1', 'C2')
csVolcano(genes(cuff_data), 'C1', 'C2')

In the linux terminal, after executing csDensity(genes(cuff_data)) command, it gave warning messages:
1: Removed 25 rows containing non-finite values (stat_density)
2: Removed 25 rows containing non-finite values (stat_density)

The reason for being different can be this removal of rows? I'm using R version 3.2.1.

Also, there is a removal of 6 rows after the execution of volcano plot.
Warning message: Removed 6 rows containing missing values (geom_point)

I'd be appreciated for any comments. Thank you!
Attached Files
File Type: ppt density plot.ppt (739.7 KB, 8 views)

Last edited by rumeys; 07-24-2015 at 04:02 PM. Reason: additional info
rumeys is offline   Reply With Quote
Old 07-24-2015, 04:04 PM   #2
rumeys
Junior Member
 
Location: AA

Join Date: Jul 2015
Posts: 3
Default

The resulting graphs:
Attached Files
File Type: pdf density scatter volcano plots.pdf (815.6 KB, 12 views)
rumeys 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 12:37 PM.


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