[BioC] Oneclass SAM analysis

[Naomi Altman]

A one-class test is correct if the data are the log expression ratios (M).

--Naomi

At 09:24 AM 1/5/2007, Jianping Jin wrote:
>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
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111