[BioC] Oneclass SAM analysis

[Jianping Jin]

Hi Elizabeth,

Did you set every measurement equal to 1s (not 1s and 2s)? As I understand 
one class analysis tests whether the mean gene expression across all 
replicates differs from zero. There is no any group comparison involved. If 
you were trying to do groups 1 and 2 comparison you probably need a 
"two-class" test.

hope this helps

Jianping


--On Thursday, January 04, 2007 3:22 PM -0600 "Brooke-Powell, Elizabeth" 
<etbp2 at borcim.wustl.edu> wrote:

> Dear list,
>
> I am wondering if you would be able help me with a problem I seem to be
> experiencing using SAM (v2.20a). I am using it through the Excel add-in,
> but the question I have is not a technical computer or programming
> problem (to my knowledge) but one about the analysis itself.
>
> When I am performing oneclass analysis of ratio data from a microarray
> experiment it seems that the oneclass analysis only likes to have odd
> numbers of data columns where each data column is a list of ratios for one
> slide in an experiment. I can get analysis done for 3,5,7,9,and 11 slides
> of data, but not 2,4,6,8,10 or 12. I am wondering if I am missing
> something about oneclass analysis, but it seems to me that you would want
> a balanced design of an experiment with even numbers of slides.
>
> Any help would be appreciated, I have tried contacting the SAM list which
> is next to useless.
>
> Happy New Year to everyone,
>
> Liz Brooke-Powell
>
> Washington University Medical School,
> Department of Molecular Microbiology,
> CB#8230, 660 S. Euclid Ave
> St. Louis, MO, 63110
>
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##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at email.unc.edu