[BioC] question about p-values in maSigPro

[Dick Beyer]

Hi Ana,

Thanks very much for the help.  All is well now.

Cheers,
Dick

------------------------------------------
Message: 12
Date: Thu, 16 Jul 2009 11:54:04 +0200
From: Ana Conesa <aconesa at cipf.es>
Subject: Re: [BioC] question about p-values in maSigPro
To: bioconductor at stat.math.ethz.ch
Message-ID: <200907161154.04821.aconesa at cipf.es>
Content-Type: text/plain;  charset="iso-8859-1"

Dear Dick

I see that your edesign matrix is not well defined. It should be like:

	Time	Replicates	Young	Old
young.0	0	1	1	0
young.8	8	2	1	0
young.16	16	3	1	0
young.20	20	4	1	0
young.32	32	5	1	0
old.0		0	6	0	1
old.8		8	7	0	1
old.16	16	8	0	1
old.20	20	9	0	1
old.32	32	10	0	1

Try this and tell me how it goes now with the analysis

Regards

Ana

On Thursday 16 July 2009 00:08:10 Dick Beyer wrote:
> 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
> 
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-- 
Ana Conesa
Bioinformatics and Genomics Department
Centro de Investigaciones Principe Felipe
Avda. Autopista Saler 16,
46012 Valencia, Spain
Phone: +34 96 328 96 80
Fax:   +34 96 328 97 01
http://bioinfo.cipf.es/aconesa
http://www.blast2go.org
==========================================


*******************************************************************************
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