[BioC] Barley cdf

[James MacDonald]

Hi Lev,

Lev Soinov wrote:
> Dear Biocore Data Team,
>    
>   I am working with Affy Barley chips at the moment. I have noticed that the order of probes in the .GIN file for these arrays is not the same as their order in the CDF environment, barley1.cdf, provided by Bioconductor. 
>   So, for example, when analysing these arrays I am getting an output such as:
>    
>   16578 EBma05_SQ003_C16_s_at
> 4886 Contig1579_s_at
>    
>   However, in the barley .GIN file these probes have different order numbers.
>   Is it OK, or is it a sign that probes were misplaced/misnumbered in the barley1.cdf?
>   Is it a reason for concern?

What exactly is a .GIN file? And what do you mean by order number?

We use the .CDF file supplied by Affymetrix to create the cdf packages, 
utilizing the mapping in that file to decide what the (x,y) location of 
each probe is. Literally thousands of people have been using these for 
over five years now, and nobody has claimed they are anything but 
accurate, so my assumption would be that they truly are accurate. But if 
you have any data that might indicate something different, I would be 
interested to see it.

Best,

Jim


>    
>   Thank you in advance.
>   Looking forward to hearing from you,
>   Lev.
>    
> 
>        
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-- 
James W. MacDonald, MS
Biostatistician
UMCCC cDNA and Affymetrix Core
University of Michigan
1500 E Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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