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 [j...@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: iani...@umkc.edu
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--
Jennifer Jackson
http://galaxyproject.org
--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
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