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 of -qqvalue-.
The -qqvalue- package is described as below on my website. The new version adds a new option -bestof()-, which specifies that the input P-values should be assumed to be the smallest P-values in a greater superset of P-values, whose number is specified by the -bestof()- option, and that the quasi-q-values should therefore be made more conservative (ie larger) accordingly. This is useful if the input P-values are the highlights of a genome scan reported in the literature, and the total number of P-values is reported, but not the individual P-values themselves.
I would like to acknowledge some very helpful advice from Gordon K. Smyth of the Walter and Eliza Hall Institute, Australia, who is one of the authors of the R package -p.adjust-, which formed the original inspiration for -qqvalue-.
Best wishes (and Happy New Year)
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: [email protected]
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.
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package qqvalue from http://www.imperial.ac.uk/nhli/r.newson/stata10
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TITLE
qqvalue: Generate quasi-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 quasi-q-values
corresponding to these P-values, calculated by inverting a
nultiple-test procedure specified by the user. These
quasi-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
quasi-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: 04january2010
Stata-Version: 10
INSTALLATION FILES (click here to install)
qqvalue.ado
qqvalue.sthlp
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