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Re: st: ANOVA Posthocs


From   Roger Newson <r.newson@imperial.ac.uk>
To   "statalist@hsphsun2.harvard.edu" <statalist@hsphsun2.harvard.edu>
Subject   Re: st: ANOVA Posthocs
Date   Mon, 25 Oct 2010 13:57:44 +0100

I would advise -multproc- users to check out the -qqvalue- package, also downloadable from SSC. -qqvalue- (like the R package -p.adjust-) outputs a frequentist q-value for each p-value, instead of outputting a discovery set.

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 22/10/2010 21:52, Ploutz-Snyder, Robert (JSC-SK)[USRA] wrote:
Yes David, we are going to run FDR through -multproc- on these t-tests as a second step. I should have mentioned this originally...

Al hit on our larger philosophical question as well.  But either way I'd like to be able to capture p-values from post-hoc comparisons--whether Scheffe, Tukey HSD, Tukey-Kramer, or otherwise.

Rob


-----Original Message-----
From: owner-statalist@hsphsun2.harvard.edu [mailto:owner-statalist@hsphsun2.harvard.edu] On Behalf Of Airey, David C
Sent: Friday, October 22, 2010 2:52 PM
To: statalist@hsphsun2.harvard.edu
Subject: re: st: ANOVA Posthocs

.

Maybe if you are doing 40*6=240 pairwise comparisons, do you want to consider controlling the false discovery rate? Along these lines, if you are doing oneway ANOVAs, why not use -regress- with the -test- command (http://www.stata.com/support/faqs/stat/test1.html) and -post- to file as you run through the genes and then submit the p-values to one of Roger Newson's packages like -smileplot or -qqvalue-?


Greetings Statalisters.

I am working on a multiple comparison problem comparing Y by Group with 4 groups, but I have MULTIPLE Y's that I need to consider because my Y's represent fold-increases in gene expression data and I'm working with over 40 genes...

So in this effort, I'd like to run Oneway ANOVAs of Y by Group for each of my genes, capture the Pairwise comparisons among my groups into a separate dataset, and repeat this with a loop for each of the genes of interest.

Ideally I'd like to use the Tukey-Kramer Pairwise user-written command (thanks Phil Enders), however that does not provide p-values in the screen output or any matrix in the return list.

An alternative would be to use the Scheffe posthoc option to -oneway- but I can't figure out how to steal those p-values either?

Any thoughts on how to grab these p-values?
Much appreciated...
Rob



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