[BioC] Maanova

[Loren Engrav]

Two questions please about maanova

> sessionInfo()
R version 2.9.0 (2009-04-17)
i386-apple-darwin9.6.0

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] maanova_1.14.0

Question 1
I enter
> ftest.Breed.mix_1000perm081109F1Fs_fdrtest <-
adjPval(ftest.Breed.mix_1000perm081109F1Fs, method = 'adaptive')
And all is fine
I enter
> ftest.Breed.mix_1000perm081109F1Fs_fdrtest <-
adjPval(ftest.Breed.mix_1000perm081109F1Fs, method = 'stepdown')
And I get
Error in fdr(x, method) :
Need to specify FDR method (stepup, adaptive, stepdown, or jsFDR). To use
jsFDR, one needs to install qvalue() package

Question 2
I enter
> ftest.Breed.mix_1000perm081109F1Fs_fdrtest <-
adjPval(ftest.Breed.mix_1000perm081109F1Fs, method = 'adaptive')
And all is fine
I enter
> ttest.Breed.mix_1000perm081109F1Fsweek1_fdr2 <-
adjPval(ttest.Breed.mix_1000perm081109F1Fsweek1, method = 'adaptive')
And it processes Ok but
All of the Fs.adjPvalperm are the same value,  0.999901839

What am I doing wrong?
Thank you

-- 
Loren Engrav, MD
Professor and Chief, Plastic Surgery, 1977-2001
Associate Director, Burn Center, 1977-2001
Univ Washington
Seattle