Go Back   SEQanswers > Applications Forums > RNA Sequencing

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 FPKM >>> Cuffdiff FPKM peromhc Bioinformatics 6 10-17-2012 01:07 PM
Cufflinks and cuffdiff FPKM values combiochem Bioinformatics 12 10-13-2012 11:37 PM
cuffdiff: same run but different FPKM, your thoughts? tdm Bioinformatics 0 01-31-2011 12:58 PM

Thread Tools
Old 11-14-2011, 02:04 PM   #1
Junior Member
Location: Nevada

Join Date: Mar 2011
Posts: 1
Default Cuffdiff FPKM and test statistic calculations

Hello, I have been lurking here a bit, but haven't posted yet, so bear with me.

I am trying to recreate the calculations of FPKM and the test statistic performed by uffdiff on two sample genes in order to better understand how my RNA-seq data has been tested (and thus better explain my data). I have been reading through the supplemental information from the paper linked on the Cufflinks website (Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation; Nature Biotechnology 28,511515(2010)doi:10.1038/nbt.1621), and I have been able to get through part of the calculations, but am still stumped.

To calculate FPKM, I am using the following formula:

(10^9)*Xg*(gamma t)

Xg is the number of fragments aligned to the gene locus (g),
gamma t is the maximum likelihood estimate of the probability of selecting a fragment from a transcript (t) coming from that gene locus
~l(t) is the adjusted transcript length
Σ from i=1 to t(i)) [F(i)(l(t)-i+1)]
F(i) = probability that the fragment has a length i
l(t) = the transcript length
M is the total number of fragments mapped in that sample

My sample is run with single-end reads 50 bp long, so I simplified the ~l(t) to the transcript length - 49, and we ran cuffdiff using a GTF file that contains only the loci for one transcript for each gene, so I think gamma should be 1. One of my lab members wrote a program that assigns raw reads to individual genes, so I am using the reads from this program for the raw reads in the FPKM calculation. Using this data I get pretty close to the FPKM calculated:

gene   Reads A   Reads B    Cuff A	Cuff B             Calc A        Calc B
A	2	81        0.021956	0.823028        0.02116         0.795515
B	1	40        0.007541	0.279201        0.007374        0.273778
The difference is most likely from my assumption that the ~l(t) is only looking at the 50 bp read length, or the assumption that gamma is 1.

From this, I get into much more complicated math when trying to recreate the test statistic. The formula for the test statistic, from the supplemental data, is:

[log(Xa)+log(gamma a)+ log(Mb) - log(Xb) - log(gamma b) - log (Ma)]
SQRT[ (psi a*(1+Xa)*(gamma a)^2)/(Xa*(gamma a)^2)+ (psi b*(1+Xb)*(gamma b)^2)/(Xb*(gamma b)^2)]

Where psi is a variance-covariance matrix that estimates the covariance between gamma (tk) and gamma (tl). As far as I can tell, tk and tl come from Tophat, which splits a read of length l into two smaller reads of length k in order to align across splice junctions. (This may be completely off base)

When I run the equations using these assumptions, though, I get a value far off from the test statistic calculated by Cuffdiff:

Gene      T stat	     Cufflinks t-stat
A          0.99128963	-3.42295
B          0.898803344	-3.07139

So, I suppose my question is, is there a way for me to calculate (or even estimate) the psi function? Am I making faulty assumptions?

I apologize if this question has been addressed in a previous thread. I did try to find the answer in the archives before asking here.
Thank you
PRingler is offline   Reply With Quote
Old 07-03-2012, 10:29 AM   #2
Location: Cincinnati

Join Date: Jan 2012
Posts: 14

Does some one has an answer for the second part of the question ?
Portah is offline   Reply With Quote
Old 10-16-2012, 02:47 AM   #3
Location: uk

Join Date: Jul 2012
Posts: 56

Hi PRinlgler,
did you come up with a solution?
I'm also quite new and tried to understand what is the mathematical process from cufflinks to cuffdiff...why are the fpkm in cufflinks differnt from those given in cuffdiff??

IBseq is offline   Reply With Quote

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 01:11 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO