[BioC] Oneclass SAM analysis

[Jianping Jin]

It is odd. I am not sure how you know the plug-in just took the odd numbers 
of columns?  I would run the sample data (came along with the SAM plug-in) 
for one class test and see how it works. Or you may need to update the 
plug-in to the current version and try it out.
Jianping.

--On Friday, January 05, 2007 9:34 AM -0600 "Brooke-Powell, Elizabeth" 
<etbp2 at borcim.wustl.edu> wrote:

> Jianping,
>
> Thank you for getting back to me, I do set all of the array column headers
> to 1 as all of the biological comparisons are the same in the same ratio
> orientation. It has to do with the number of columns of data in total on
> the worksheet, it only likes odd numbers of arrays.
>
> Liz
>
>
> -----Original Message-----
> From: Jianping Jin [mailto:jjin at email.unc.edu]
> Sent: Friday, January 05, 2007 8:25 AM
> To: Brooke-Powell, Elizabeth; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Oneclass SAM analysis
>
> 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
>
>
>



##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
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University of Chapel Hill
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Phone: (919)843-6105
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E-Mail: jjin at email.unc.edu