Hello,

 

I am running SPIA (downloaded from the Bioconductor source repository
8/5/2010) on Affymetrix MoGene data collected for mouse using the following
command:

 

res = spia(de = DE, all = ALL, organism = "mmu", nB = 2000, plots = FALSE,
beta = NULL)

 

The procedure runs to completion and produces results and shows several
pathways with significant perturbation, but the pSize and NDE are always
equal for every pathway evaluated - the top 10 are listed below.  

 

                             Name
ID            pSize     NDE        tA                           pNDE
pPERT

1              Cytokine-cytokine receptor int                  04060    44
44           17.81364905       1              0.000005

2              Chemokine signaling pathway                    04062    44
44           70.55024083       1              0.000005

3              Antigen processing and present                04612    19
19           19.20487487       1              0.000005

4              Intestinal immune network for                  04672    17
17           11.53587339       1              0.000005

5              Olfactory transduction
04740    43            43           -45.40999859      1
0.000005

6              Type I diabetes mellitus                                04940
13            13           17.52273370       1              0.000005

7              Autoimmune thyroid disease                     05320    13
13           17.48652443       1              0.000005

8              Systemic lupus erythematosus                  05322    28
28           21.08154901       1              0.000005

9             Allograft rejection
05330    14            14           17.65594344       1
0.000005

10           Graft-versus-host disease                           05332    12
12           17.59478491       1              0.000005

 

 

This must be an error - Any thoughts on why I might see this?  

 

Thanks!

Will

 

 

______________________________

William S. Bush, PhD, MS

Assistant Professor

Center for Human Genetics Research

Department of Biomedical Informatics

Vanderbilt University

Nashville, TN 37232

 

 


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