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Re: st: New version of -qqvalue- for SSC


From   Roger Newson <r.newson@imperial.ac.uk>
To   "statalist@hsphsun2.harvard.edu" <statalist@hsphsun2.harvard.edu>
Subject   Re: st: New version of -qqvalue- for SSC
Date   Sun, 8 Aug 2010 19:34:27 +0100

Sorry about this. This message was intended for Kit Baum, and not for Statalist (where attachments are banned). The new version referred to is currently available on my website, but I have now sent a copy to Kit Baum for distribution on SSC when he returns to Boston,

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.

On 08/08/2010 19:27, Roger Newson wrote:
Hello Kit

Please find attached the latest version of the -qqvalue- package
(defined as below on my website) for distribution on SSC when you return
to Boston after 12 August.

The new version replaces the terminology "quasi-q-value" with "q-value"
in the .pkg file, in the on-line help, and in the labels of the
generated variables. I was advised by Gordon Smyth (the author of the R
package -p.adjust-, which does a similar job in R) that the "quasi-" is
not really necessary, as people he knows just call them "q-values". I
have therefore altered the terminology to remove the "quasi-", but use
the term "frequentist q-values" when I need to make a distinction
between the frequentist q-values produced by -qqvalue- and -p.adjust-
and the original empirical Bayesian q-values defined by John Storey.

Best wishes (and thanke in advance)

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
--------------------------------------------------------------------------------------------------
(click here to return to the previous screen)


On 31/07/2010 14:06, Christopher Baum wrote:
SSC Archive updates will be on hold 1-12 August while I am traveling. Materials sent during that time will be processed after 12 August.

Kit Baum

Research Papers in Economics (RePEc)
http://repec.org




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