Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Different fpkm values for cuffdiff and cuffcompare madsaan Bioinformatics 3 12-12-2012 04:14 PM
Different FPKM values of cufflinks and cuffdiff mrfox Bioinformatics 5 10-17-2012 01:10 PM
Cufflinks and cuffdiff FPKM values combiochem Bioinformatics 12 10-13-2012 11:37 PM
Cuffcompare/cuffdiff changes FPKM values of same BAM in sequential runs SEQond RNA Sequencing 2 10-17-2011 06:42 AM
Different FPKM values of cufflinks and cuffdiff in latest version mrfox Bioinformatics 1 11-23-2010 05:23 AM

Thread Tools
Old 04-11-2011, 05:43 AM   #1
Location: Sweden

Join Date: Nov 2009
Posts: 12
Question Cuffdiff and zero FPKM values give enormous log ratio

Hi all,
I'm new to RNA seq and I'm working with TopHat - Cufflinks - Cuffcompare - Cuffdiff pipeline.
I use Cufflinks without annotation and then Cuffcompare for two samples with annotation. I put the results of Cuffcompare (transcripts.combined.gtf) to Cuffdiff as input. Is this the right way?

I have results from cuffdiff for differential expression testing. As a result for DE testing it provides the following measure: ln(FPKMx/FPKVy) for ratio for the gene between two samples X and Y. If for gene A in sample X FPKMx = 2 and for the sample Y FPKMy=0, then the ratio is like 1,79 E306, so enormously big
How do you deal with it?

Any ideas are very welcome!
altodor is offline   Reply With Quote
Old 04-15-2011, 02:24 AM   #2
Junior Member
Location: Uppsala University, Sweden

Join Date: Sep 2010
Posts: 8


Regarding the huge ratios, i think they are hard to avoid. There is no other way to handle the scenarios where you have a gene that is switched on/off, that i know of.

If you were to plot your ratio values, you would likely see most of them around 0 - a couple of thousand perhaps, and some scattered outliers with ridiculous high values. You can then set a suitable cutoff and say that all genes with a ratio higher than X (say 1e10 or 1e20) are genes that have been turned off or on. It is pointless to sort them with respect to their ratio size, since they all should have Inf.

Computers don't like to divide by 0, so a small number (like 1e-500 or so) has been added to the FPKMy in the division to keep the program from crashing, since many programming languages can't handle infinite numbers.

dahlo is offline   Reply With Quote
Old 04-15-2011, 08:01 AM   #3
Location: Sweden

Join Date: Nov 2009
Posts: 12

Thank you!
altodor is offline   Reply With Quote

cuffdiff, cufflinks, differential expression, fpkm ratio, read counts

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 08:43 AM.

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