[BioC] U133A probe sequences...?

[James W. MacDonald]

Hi Dario,

Dario Greco wrote:
> dear all,
> 
> I am puzzling with a quite stupid problem, so don't blame me if the  
> answer is something very simple, please.
> 
> I am working with the affy HG-U133A probe sequences. both the  
> hgu133aprobe package and the file available in affymetrix.com give 16  
> probe sequences per each probe set.
> but I would expect only 11.
> 
> what is the explanation?

There are many different probeset lengths for any given Affy chip. They 
just report the most common.

 > a <- as.data.frame(hgu133aprobe)
 > b <- as.factor(a[,4])
 > table(table(b))

     8    10    11    13    14    15    16    20    69
     1     1 21748     4     4     2   482    40     1

So there are 482 probesets that have 16 probes, but the vast majority 
have 11.

HTH,

Jim


> 
> thanks in advance for your help..!
> 
> dario
> 


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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