[BioC] question about p-values in maSigPro

[Dick Beyer]

Hello Ana,

I've been using the maSigPro package for some time-course data and I was wondering about how to interpret the output of p.vector().

I have two groups, young and old, 5 time points for each, 0,8,16,20,32, and no replicates.  I'm trying, for example, degree=2.  My design matrix is:

design
$dis
          tim tim2
young.0    0    0
young.8    8   64
young.16  16  256
young.20  20  400
young.32  32 1024
old.0      0    0
old.8      8   64
old.16    16  256
old.20    20  400
old.32    32 1024

$groups.vector
[1] "age" "age"

$edesign
          tim repl age
young.0    0    1   0
young.8    8    1   0
young.16  16    1   0
young.20  20    1   0
young.32  32    1   0
old.0      0    1   1
old.8      8    1   1
old.16    16    1   1
old.20    20    1   1
old.32    32    1   1

These are affy mouse gene ST arrays.  In order to understand how to interpret the p.vector() p-values, I made a few genes have identical young and old expression values, for example, for one probe:

age.time	log2 expr
young.0	        5.969643
young.8	        4.260117
young.16	4.650527
young.20	4.441443
young.32	4.955249
old.0	        5.969643
old.8	        4.260117
old.16	        4.650527
old.20	        4.441443
old.32	        4.955249

What puzzles me is the p-value from the p.vector() fit is 0.006862036.  I expected it to be about 1.  I must be doing something wrong.

My call to p.vector() is:

fit <- p.vector(myData, design, Q = 1, min.obs = 3)

where myData has 10 columns.

sessionInfo()
R version 2.9.0 (2009-04-17) 
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
[1] maSigPro_1.16.0 Biobase_2.4.0

loaded via a namespace (and not attached):
[1] limma_2.18.0 Mfuzz_2.2.0

I'd appreciate any help or suggestions you could give me.

Thanks very much,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer