[BioC] Oneclass SAM analysis

[Brooke-Powell, Elizabeth]

Actually I tested it. I had 12 slides worth of data, and tried to run SAM
and it choked, so I went and tried with only 3 slides which worked and
slowly increased the numbers of columns by one each time up to 12. Every
time I had an even number of slides it choked and every time I had an odd
number of columns; at least up to 11; it worked fine. 

I have what is the latest version according to the SAM website, but it was a
curious problem and wondered if there was a mathematical/statistical reason
as to why even numbers of columns don't work. From experimental design
aspects it is better to have a balanced design with an even number of
hybridizations.

Liz 

-----Original Message-----
From: Jianping Jin [mailto:jjin at email.unc.edu] 
Sent: Friday, January 05, 2007 11:06 AM
To: Brooke-Powell, Elizabeth; bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] Oneclass SAM analysis

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
>
>