Hooiveld, Guido | 8 Mar 10:12 2013
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Re: Testing for logFC significantly larger than threshold; or: calculating confidence intervals in limma

Hi,
Is the function 'treat' in limma not doing what you are looking for?
http://bioinformatics.oxfordjournals.org/content/25/6/765.abstract

Regards,
Guido

-----Original Message-----
From: bioconductor-bounces@...
[mailto:bioconductor-bounces@...] On Behalf Of January Weiner
Sent: Friday, March 08, 2013 09:28
To: Bioconductor mailing list
Subject: [BioC] Testing for logFC significantly larger than threshold; or: calculating confidence
intervals in limma

Dear all,

normally, one tests whether a difference between the experimental conditions (expressed as logFC) is
significantly different from 0.
Thus, limma provides a p-value (or adjusted p-value) for the test where the H_0 is that logFC == 0, and H_alt
is that logFC =/= 0.

I would like, however, to test the hypothesis abs( logFC ) <= T and the alternative abs( logFC ) > T, where T is
an arbitrary threshold.
For example, T=1 for genes for which the change of expression is significantly more than twofold, either way.

Note that this is not the same as choosing genes for which abs( lfc )
> 1 and adj.P.Val < 0.05. A gene might have an estimated logFC over 1,
and the logFC might be significantly different from 0, but it can have a variance large enough for the logFC
not be significantly higher than 1.

An alternative is to calculate the 0.05 confidence interval for each estimated logFC, since that
automatically gives the answer that I'm looking for.

Clearly, I can do the analysis myself, for example calculating the regular t-statistic, but I would like to
take advantage of the moderated t-statistic present in limma as well as all the facilities for creating
complex contrasts.

Kind regards,

January

--
-------- January Weiner --------------------------------------

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