[BioC] P values

Naomi Altman naomi at stat.psu.edu
Tue Jul 12 23:27:21 CEST 2005

If you are using TopTable, then you are obtaining the q-value, not the 
p-value.  The q-value does not have a 1-1 relationship with the t-value.


At 09:53 AM 7/12/2005, Tai, Helen wrote:
>I have been having problems with getting P values when using limma with affy
>data from the Arabidopsis AG arrays but not the ATH1 arrays.  All the P
>values from the AG data are 0.999984 even though the t statistic is varying
>in value.  Has anyone else had this problem?
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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