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st: RE: Genome-wide associations in Stata

From   "Newson, Roger B" <>
To   <>
Subject   st: RE: Genome-wide associations in Stata
Date   Fri, 9 May 2008 16:26:07 +0100

I personally haven;t as yet done any microarray analyses in Stata.
However, I have done a lot of analyses in Stata, in genetics and
otherwise, involving mass-production of multiple comparisons (although
not as many as 1,000,000 SNPs at a time, which I understand is becoming
routine with this year's microarray technology). And I wrote the
-smileplot- package (downloadable from SSC) to implement a range of
multiple-test procedures, including the Simes procedure, which controls
the false discovery rate (FDR). My Stata Journal paper on multiple-test
procedures can be downloaded from

What aspects of this fast-evolving field do you find Stata inadequate
for? And what does R do better?

Best wishes


Roger B Newson
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
Web page:
Departmental Web page:

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

-----Original Message-----
[] On Behalf Of
Sent: 09 May 2008 15:25
Subject: st: Genome-wide associations in Stata

Dear statalister,

Does anyone have experience in running genome-wide association analyses

Toby Andrew has provied useful tips for genome-wide linkage analysis,
I would like to know in more detail your current experience in running
these sort of computer intensive stuff. I got frustrated with Stata
regarding its complete lack of programs to analyze microarray data. To
it bluntly, Should I forget using Stata in these high-throughput
experiments from now on and rely on R only?

Thank you in advance!



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