[BioC] CAMERA for non-directional gene sets
dwu at fas.harvard.edu
Tue Sep 4 17:40:16 CEST 2012
Thank you for your interest in using CAMERA. It has lots of good feathers, holding correct false positive rate and having good power. It can be used when you have multiple gene sets, e.g., GO as you mentioned.
Currently, the default test statistics for individual genes is the moderated t, which is a variant of the ordinary t. See Smyth 2004. (http://www.statsci.org/smyth/pubs/ebayes.pdf)
It is up to the user whether ranks (of the moderated t) should be used or not.
Of course, it is easily to edit the code to allow log fold change to represent the change of the individual genes. What other statistics for individual genes will you be interested in using?
It is also worth noting that, according to other users, it is safe to set “allow.neg.cor=FLASE”, to let correlation be zero when the actual calculated correlation is negative.
Gordon may also have some insight regarding your question.
Enjoy using CAMERA.
Harvard University, Statistics Department
Harvard Medical School
Science Center, 1 Oxford Street, Cambridge, MA 02138-2901 USA
From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] On Behalf Of Simon de Bernard [simon.debernard at altrabio.com]
Sent: Monday, September 03, 2012 6:58 AM
To: bioconductor at r-project.org
Subject: [BioC] CAMERA for non-directional gene sets
The publication for CAMERA (http://nar.oxfordjournals.org/content/early/2012/05/24/nar.gks461.full) mentions using the average absolute-logFC as a statistics for "non-directional" gene sets.
This would seem like the appropriate approach for gene sets from e.g. the GO database.
However I was unable to find how to use anything other than logFC or its rank from the camera documentation in limma.
Have I missed something?
Thanking you in advance,
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