SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Cufflinks / Cuffdiff problem Morten Bioinformatics 42 07-13-2013 11:51 PM
Problem about splicing.diff from cuffdiff leifive RNA Sequencing 0 03-18-2013 02:00 AM
Running problem with cuffdiff john_nl Bioinformatics 2 02-16-2012 12:21 PM
Cuffdiff - ouput problem ytmnd85 Bioinformatics 12 12-02-2011 09:10 AM
Problem with Cuffdiff honey RNA Sequencing 3 01-04-2011 10:02 PM

Reply
 
Thread Tools
Old 07-20-2013, 10:05 AM   #1
sazz
Member
 
Location: Istanbul, Turkey

Join Date: Oct 2012
Posts: 28
Default Cuffdiff p-value problem

Hello all,

I run the Tuxedo pipeline to find differentially expressed genes btw 2 phenotypes (3 replicates for each) but in the end I get p-values limited to "0.00005" in CuffDiff output, nothing smaller; 1264 of 23779 genes (human) have that limitation so this is not their actual p-value, most of them should be much more significant. I have the latest version of CuffDiff (2.1.1). In the older versions I didn't have such a problem.

I don't know what I miss but I appreciate if you can help.
sazz is offline   Reply With Quote
Old 07-20-2013, 12:26 PM   #2
Gus
Member
 
Location: Irvine CA, USA

Join Date: Dec 2009
Posts: 29
Default

That is crazy because I was logging on to ask this exact question.

I am doing the same experiment in four species and i do not have the problem with all species. I will attach links to the resulting volcano plots from a species with the problem.

Can anyone PLEASE offer explanations I am at a loss...

http://previews.figshare.com/1057598...ew_1057598.jpg
__________________
In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.
--Stephen Jay Gould
Gus is offline   Reply With Quote
Old 07-20-2013, 12:34 PM   #3
Gus
Member
 
Location: Irvine CA, USA

Join Date: Dec 2009
Posts: 29
Default

OK i got so excited that someone was asking the same thing as me that I neglected to do a search first...

Upon searching, perhaps the answer is in this thread: http://seqanswers.com/forums/showthr...fdiff+p-values

Sounds like it is due to a change in the way cuffdiff does its p-values by default (now through empirical sampling? ).

Can others confirm this?

I will need to go back and see which version I used for the species that does not show this cut off.

Gus


PS: I checked my records and this is indeed the case. The species that doe snot show the cutoff was run with 2.0.2.
__________________
In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.
--Stephen Jay Gould

Last edited by Gus; 07-20-2013 at 12:39 PM. Reason: answered a question posed in original response.
Gus is offline   Reply With Quote
Old 07-20-2013, 12:44 PM   #4
sazz
Member
 
Location: Istanbul, Turkey

Join Date: Oct 2012
Posts: 28
Default

Thanks Gus, I am a little relieved.
sazz 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 05:40 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO