[BioC] multtest MTP raw P values = 0

[Timur Shtatland]

Dear all,

I used MTP from the multtest package to compute bootstrap based raw
and adjusted t-test P values (group 1 = 7 samples, group 2 = 3
samples). Why are some raw P values in the output exactly zero?

I could not change this by using scientific notation, with varying
number of significant digits. In the example below, 10 digits are
used; increasing this does not make a difference. I expected all P
values > 0, with the minimum P value determined by the number of
bootstrap iterations, here 1000. Hence the raw P value minimum should
be 1e-03, as indeed the lowest *positive* P values are.

Another question is: why some raw P values that are *equal* correspond
to adjusted P values that are *different*?

For example, raw P = 1e-03 corresponds to adjusted P = 8.4e-02,
8.6e-02, etc.

I could not find the answer in the MTP help page, its vignettes, FAQ,
etc. A similar, but not identical, problem was reported on this
mailing list before, without a solution:

https://stat.ethz.ch/pipermail/bioconductor/2007-December/020492.html

Thank you for your help.

Best regards,

Timur
--
Timur Shtatland, PhD
Center for Molecular Imaging Research
Massachusetts General Hospital
149 13th Street, Room 5408
Charlestown, MA 02129
tshtatland at mgh dot harvard dot edu

############################################################

 > B <- 1000
 > seed <- 99
 > TTBoot <- MTP(X=esetGcrmaExprsFiltered, Y=TT, test =  
"t.twosamp.unequalvar", alternative = "two.sided", typeone="fdr",  
method="ss.maxT", fdr.method="conservative", B=B, seed=seed)

running bootstrap...
iteration = 100 200 300 400 500 600 700 800 900 1000

 > print(TTBoot)
	Multiple Testing Procedure

Object of class:  MTP
sample size = 10
number of hypotheses = 5413

test statistics = t.twosamp.unequalvar
type I error rate = fdr
nominal level alpha = 0.05
multiple testing procedure = ss.maxT

Call: MTP(X = esetGcrmaExprsFiltered, Y = TT, test =  
"t.twosamp.unequalvar",
     alternative = "two.sided", typeone = "fdr", fdr.method =  
"conservative",
     B = B, method = "ss.maxT", seed = seed)

Slots:
             Class    Mode  Length Dimension
statistic numeric numeric    5413
estimate  numeric numeric    5413
sampsize  integer numeric       1
rawp      numeric numeric    5413
adjp      numeric numeric    5413
conf.reg    array logical       0     0,0,0
cutoff     matrix logical       0       0,0
reject     matrix logical    5413    5413,1
nulldist   matrix numeric 5413000 5413,1000
call         call    call      10
seed      integer numeric       1
...

 > MTPRes <- data.frame(PRaw=TTBoot at rawp, PAdj=TTBoot at adjp)

 > print(format(subset(MTPRes[order(MTPRes$PRaw, MTPRes$PAdj), ],  
PAdj < 0.1), digits=10, scientific=TRUE))
              PRaw            PAdj
202508_s_at 0e+00 0.000000000e+00
203130_s_at 0e+00 0.000000000e+00
206780_at   0e+00 0.000000000e+00
218820_at   0e+00 0.000000000e+00
205825_at   0e+00 8.000000000e-03
203000_at   0e+00 1.400000000e-02
204465_s_at 0e+00 1.400000000e-02
206282_at   0e+00 1.400000000e-02
206502_s_at 0e+00 1.400000000e-02
208399_s_at 0e+00 1.400000000e-02
209598_at   0e+00 1.400000000e-02
209755_at   0e+00 1.400000000e-02
212805_at   0e+00 1.400000000e-02
203001_s_at 0e+00 2.400000000e-02
204811_s_at 0e+00 2.400000000e-02
205174_s_at 0e+00 2.400000000e-02
205646_s_at 0e+00 2.400000000e-02
206051_at   0e+00 2.400000000e-02
212624_s_at 0e+00 2.800000000e-02
204035_at   0e+00 3.000000000e-02
221261_x_at 0e+00 3.200000000e-02
206915_at   0e+00 3.400000000e-02
206104_at   0e+00 4.000000000e-02
210036_s_at 0e+00 5.000000000e-02
218380_at   0e+00 5.000000000e-02
213135_at   0e+00 6.200000000e-02
204870_s_at 0e+00 6.400000000e-02
218952_at   0e+00 6.400000000e-02
205120_s_at 0e+00 6.600000000e-02
211597_s_at 0e+00 6.666666667e-02
205348_s_at 0e+00 6.800000000e-02
212190_at   0e+00 7.000000000e-02
213186_at   0e+00 7.000000000e-02
203485_at   0e+00 7.200000000e-02
203572_s_at 0e+00 8.400000000e-02
209583_s_at 0e+00 8.400000000e-02
212895_s_at 0e+00 8.400000000e-02
206001_at   0e+00 8.600000000e-02
206135_at   0e+00 8.600000000e-02
212843_at   0e+00 8.600000000e-02
204059_s_at 0e+00 8.800000000e-02
210826_x_at 0e+00 9.000000000e-02
213438_at   0e+00 9.000000000e-02
218675_at   0e+00 9.000000000e-02
201116_s_at 0e+00 9.200000000e-02
203272_s_at 0e+00 9.600000000e-02
204793_at   0e+00 9.800000000e-02
204720_s_at 1e-03 8.400000000e-02
221207_s_at 1e-03 8.400000000e-02
204540_at   1e-03 8.600000000e-02
209992_at   1e-03 8.888888889e-02
210246_s_at 1e-03 9.000000000e-02

 > print(dim(esetGcrmaFiltered))
Features  Samples
     5413       10

 > sessionInfo()
R version 2.6.0 (2007-10-03)
powerpc-apple-darwin8.10.1

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

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

other attached packages:
  [1] multtest_1.18.0      affydata_1.11.3      affyQCReport_1.16.0   
geneplotter_1.16.0   lattice_0.16-5
  [6] annotate_1.16.1      AnnotationDbi_1.0.6  RSQLite_0.6-4         
DBI_0.2-4            RColorBrewer_1.0-2
[11] affyPLM_1.14.0       xtable_1.5-2         simpleaffy_2.14.05    
gcrma_2.10.0         matchprobes_1.10.0
[16] genefilter_1.16.0    survival_2.32        affy_1.16.0           
preprocessCore_1.0.0 affyio_1.6.1
[21] Biobase_1.16.1

loaded via a namespace (and not attached):
[1] KernSmooth_2.22-21 grid_2.6.0

 > version
                _
platform       powerpc-apple-darwin8.10.1
arch           powerpc
os             darwin8.10.1
system         powerpc, darwin8.10.1
status
major          2
minor          6.0
year           2007
month          10
day            03
svn rev        43063
language       R
version.string R version 2.6.0 (2007-10-03)

# platform: PowerPC G4, Mac OS 10.4.11.


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