SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
SAM: Significance Analysis of Microarrays Amative Bioinformatics 0 11-27-2012 09:41 AM
Cuffdiff DE significance of zero FPKM values jwalker_tgi Bioinformatics 7 10-13-2012 04:14 PM
Significance of an FPKM value JueFish Bioinformatics 5 10-12-2012 12:27 AM
Determining clinical significance of variants Rocketknight Bioinformatics 2 09-28-2012 09:54 AM
read numbers AND biological significance lwgbioinfor Bioinformatics 0 07-18-2011 07:13 PM

Reply
 
Thread Tools
Old 03-01-2013, 07:55 PM   #1
differential
Junior Member
 
Location: Corvallis OR

Join Date: Oct 2012
Posts: 1
Default Cuffdiff significance

Hi,

I have 3 sequenced transgenic Arabidopsis genomes (sequenced sing Tuxedo suite). I am looking for genes that exhibit significant differential expression in all 3 transgenic lines and ideally do not show significant differential expression in our WT control lines. When I use only genes that have an FDR<0.05 I get virtually no interesting genes (i.e., unknown proteins), but when I arbitrarily choose a fold change of 2 (chosen by my professor) and ignore the FDR, I get quite a few genes that are interesting to my professor.

Is there a way to justify using these genes even though cuffdiff says that the expression is insignificant?

Please let me know if this is not information, etc. I am very new at this.
differential is offline   Reply With Quote
Old 03-04-2013, 04:54 AM   #2
rboettcher
Member
 
Location: Berlin

Join Date: Oct 2010
Posts: 71
Default

Cuffdiff is known to be very stringent, especially if the variance within your groups is quite high. If you are accustomed to R, then you can try to use methods such as DESeq or edgeR for differential expression analysis, otherwise, just disregard Cuffdiff's FDR and set thresholds for fold change and overall expression and see how far you get (though I would not recommend that).
I also recently read about another RNAseq pipeline called Grape, maybe that helps you further. See http://bioinformatics.oxfordjournals.../29/5/614.long
rboettcher 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 01:37 AM.


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