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st: New version of -qqvalue- on SSC


From   Roger Newson <r.newson@imperial.ac.uk>
To   "statalist@hsphsun2.harvard.edu" <statalist@hsphsun2.harvard.edu>
Subject   st: New version of -qqvalue- on SSC
Date   Wed, 1 Sep 2010 11:38:25 +0100

Thanks to Kit Baum, a new version of the -qqvalue- package is now available for download from SSC. In Stata, use the -ssc- command to do this, or -adoupdate- if you already have an old version.

The -qqvalue- package is described as below on my website. In the new version, the term "quasi-q-value" has been replaced throughout, both in the on-line help and in the labels of the generated variables, by "q-value", or by "frequentist q-value", if I need to stress the distinction from the original empirical Bayesian q-values introduced by John Storey. I would like to thank Gordon K. Smyth(the author of the original R package -p.adjust-) for advising me that the "quasi-" was not really necessary, and thereby saving a lot of bytes of print.

I am told by the Stata Journal editors that my submitted article on -qqvalue-, giving the full methods and formulas used, is due to appear in the near future.

Best wishes

Roger


--
Roger B Newson BSc MSc DPhil
Lecturer in Medical Statistics
Respiratory Epidemiology and Public Health Group
National Heart and Lung Institute
Imperial College London
Royal Brompton Campus
Room 33, Emmanuel Kaye Building
1B Manresa Road
London SW3 6LR
UNITED KINGDOM
Tel: +44 (0)20 7352 8121 ext 3381
Fax: +44 (0)20 7351 8322
Email: r.newson@imperial.ac.uk
Web page: http://www.imperial.ac.uk/nhli/r.newson/
Departmental Web page:
http://www1.imperial.ac.uk/medicine/about/divisions/nhli/respiration/popgenetics/reph/

Opinions expressed are those of the author, not of the institution.

-----------------------------------------------------------------------------------
package qqvalue from http://www.imperial.ac.uk/nhli/r.newson/stata10
-----------------------------------------------------------------------------------

TITLE
qqvalue: Generate frequentist q-values by inverting multiple-test procedures

DESCRIPTION/AUTHOR(S)
      qqvalue is similar to the R package p.adjust.  It inputs a single
      variable, assumed to contain P-values calculated for multiple
      comparisons, in a dataset with 1 observation per comparison.  It
      outputs a new variable, containing the q-values corresponding to
      these P-values, calculated by inverting a multiple-test procedure
      specified by the user.  These q-values represent, for each
      corresponding P-value, the minimum uncorrected P-value threshold
      for which that P-value would be in the discovery set, assuming that
      the specified multiple-test procedure was used on the same set of
      input P-values to generate a corrected P-value threshold.  These
      minimum uncorrected P-value thresholds may represent familywise
      error rates or false discovery rates, depending on the procedure
      used.  Optionally, qqvalue may output other variables, containing
      the various intermediate results used in calculating the
      q-values.  The multiple-test procedures available for
      qqvalue are a subset of those available using the multproc module
      of the smileplot package, which can be downloaded from SSC.

      Author: Roger Newson
      Distribution-Date: 08august2010
      Stata-Version: 10

INSTALLATION FILES                                  (click here to install)
      qqvalue.ado
      qqvalue.sthlp
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