[BioC] Oneclass SAM analysis

[Jianping Jin]

I installed the SAM v.2.23A on a machine with the Windows XP OS and have 
never observed what you described. A problem I ever ran into was memory 
overflow. I am not a statistician, but I doubt there are any statistical 
reasons for preference of odd number of samples in one class test.

Jianping

--On Friday, January 05, 2007 11:30 AM -0600 "Brooke-Powell, Elizabeth" 
<etbp2 at borcim.wustl.edu> wrote:

> 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
>>
>>
>



##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
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