Hi Guiseppe,

This RNA-seq tutorial has an example walk-through using these tools plus links to documentation sources that can help guide you in the analysis, including the paper produced by the tool authors.
https://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise

And see:
http://cufflinks.cbcb.umd.edu/howitworks.html#hdif

In short, fold change is the log2 ratio of FPKMs between the two inputs (not simply just a FPKM). If 0, then there is no change; if 1, a 2-fold change, etc. There are also many resources online in general and specific to expression analysis that explain this in more detail. Even if these focus on microarray data, many of the underlying concepts will apply broadly to most (all?) expression analysis, regardless of the technique to obtain the primary data.

Good luck,

Jen
Galaxy team

On 11/29/12 10:10 AM, Ianiri, Giuseppe wrote:
Thank you Jennifer.
I just start working with these things, so I am wondering which minimal value of FPKM I should use in the filter tool. Do you have an advice or an example that I could look at?
Thank you 

Giuseppe Ianiri, Ph.D.
Division of Cell Biology and Biophysics

From: Jennifer Jackson [jen@bx.psu.edu]
Sent: Thursday, November 29, 2012 10:51 AM
To: Ianiri, Giuseppe
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] filter for +/- 2-fold difference in expression levels

Hello Giuseppe,

Fold is included in the Cuffdiff output. Section "Differential expression tests", first file, column #9.
http://cufflinks.cbcb.umd.edu/manual.html

A tool like " Filter and Sort -> Filter" could be used to subset specific values.

Hopefully this helps,

Jen
Galaxy team

On 11/29/12 5:35 AM, Ianiri, Giuseppe wrote:
Hey guys,
I have my Cuffdiff output and I was trying to figure out how to get the data I need.
I am interested in the outputs Transcript and Gene differential expressed. Does anyone know how to filter for +/- 2-fold difference in expression levels?
Thank you

Giuseppe Ianiri, Ph.D. 
Division of Cell Biology and Biophysics
School of Biological Sciences
5100 Rockhill Road
University of Missouri-Kansas City
Kansas City, MO 64110
Email: ianirig@umkc.edu



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Jennifer Jackson
http://galaxyproject.org