[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

st: New version of -qqvalue- on SSC

From   "Newson, Roger B" <[email protected]>
To   "'[email protected]'" <[email protected]>
Subject   st: New version of -qqvalue- on SSC
Date   Mon, 4 Jan 2010 22:18:53 +0000

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 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
Tel: +44 (0)20 7352 8121 ext 3381
Fax: +44 (0)20 7351 8322
Email: [email protected] 
Web page:
Departmental Web page:

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

package qqvalue from

      qqvalue: Generate quasi-q-values by inverting multiple-test procedures

      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)
(click here to return to the previous screen)

*   For searches and help try:

© Copyright 1996–2024 StataCorp LLC   |   Terms of use   |   Privacy   |   Contact us   |   What's new   |   Site index