[BioC] multtest MTP raw P values = 0

Timur Shtatland tshtatland at MGH.HARVARD.EDU
Fri Feb 29 19:37:28 CET 2008

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:


Thank you for your help.

Best regards,

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 =  
     alternative = "two.sided", typeone = "fdr", fdr.method =  
     B = B, method = "ss.maxT", seed = seed)

             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)


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
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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