[BioC] CAMERA for non-directional gene sets

[Simon de Bernard]

Dear Di,

thanks for your answer.

> Thank you for your interest in using CAMERA. It has lots of good feathers, holding correct false positive rate and having good power.

That's why it piqued my interest ;-)

>  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?

Sorry for mixing up logFC and moderated t. However, isn't it still an approach only appropriate for "directional" gene sets?

Suppose I have a gene set for which I know that genes should be differentially expressed but not necessarily in the same direction. If half the genes in my set have a statistic of -10 and the other half of +10, won't the current implementation give me p=1 when I would expect significance?

Best regards,

Simon.

> 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.
> 
> Di
> 
> 
> 
> 
> ----
> Di Wu
> Postdoctoral fellow
> Harvard University, Statistics Department
> Harvard Medical School
> Science Center, 1 Oxford Street, Cambridge, MA 02138-2901 USA