[BioC] P values

Stefano Calza stecalza at tiscali.it
Wed Jul 13 18:08:19 CEST 2005

This is surprising to me. topTable returns corrected p-value, but to my knowledge not using the q-value algorithm. Is there a new function TopTable? Not in the release version.


On Tue, Jul 12, 2005 at 05:27:21PM -0400, Naomi Altman wrote:
<Naomi>If you are using TopTable, then you are obtaining the q-value, not the 
<Naomi>p-value.  The q-value does not have a 1-1 relationship with the t-value.
<Naomi>At 09:53 AM 7/12/2005, Tai, Helen wrote:
<Naomi>>I have been having problems with getting P values when using limma with affy
<Naomi>>data from the Arabidopsis AG arrays but not the ATH1 arrays.  All the P
<Naomi>>values from the AG data are 0.999984 even though the t statistic is varying
<Naomi>>in value.  Has anyone else had this problem?
<Naomi>>Bioconductor mailing list
<Naomi>>Bioconductor at stat.math.ethz.ch
<Naomi>Naomi S. Altman                                814-865-3791 (voice)
<Naomi>Associate Professor
<Naomi>Bioinformatics Consulting Center
<Naomi>Dept. of Statistics                              814-863-7114 (fax)
<Naomi>Penn State University                         814-865-1348 (Statistics)
<Naomi>University Park, PA 16802-2111
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Stefano Calza, PhD
Sezione di Statistica Medica e Biometria
Dip. di Scienze Biomediche e Biotecnologie
Università degli Studi di Brescia - Italia
Viale Europa, 11 25123 Brescia
email: calza at med.unibs.it
Telefono/Phone: +390303717532
Fax: +390303717488

Section of Medical Statistics and Biometry
Dept. Biomedical Sciences and Biotechnology
University of Brescia - Italy

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