[BioC] Affy array layout

[Kasper Daniel Hansen]

There are several "QC" probes on an Affy array. QC is a term Affy uses  
and it is (I would say) a bit different than what most stat people  
would think of. Basically, QC probes contains really bright probes  
that are used for gridding the image. The QC probes also contains  
other types of probes. These probes are typically at the edge of the  
array, although for larger arrays they could be all over.

You should read up a bit on this. I recommend reading the affymetrix  
file format specifications. Also take a look at an ASCII CDF file so  
you get an idea about what goes on.

affxparser has special routines for reading these QC probes and I know  
you can do it with affyio as well. No-one uses them for anything,  
besides the images processing - at least as far as I know.

Kasper

On Jul 17, 2008, at 9:56 PM, <Nathan.Watson-Haigh at csiro.au> <Nathan.Watson-Haigh at csiro.au 
 > wrote:

> I want to generate some quality control plots for Affymetrix arrays
> (initially bovine and Arabidopsis).
>
> I'd like to know more about the layout of probes on the array. For
> instance, when I get the pm and mm probes separately, the number
> returned is different from that returned by intensity(), why is this?:
>
>> dim(pm(AffyBatch))[1] + dim(mm(AffyBatch))[1]
> [1] 531254
>> dim(intensity(AffyBatch))[1]
> [1] 535824
>
> Also, there doesn't appear to be any PM or MM probes on the outside  
> edge
> of the array, i.e. column/row 1 and n (where n is the size of the  
> array)
> - is there any reason for this? What are the probes on the outside  
> edge
> supposed to measure?
>
> Cheers,
> Nathan
>
>
> -------------------------------------------------------------
> Dr. Nathan S. Watson-Haigh        (publish under Haigh, N.S.)
> OCE Post Doctoral Fellow
> CSIRO Livestock Industries
> J M Rendel Laboratory
> Rockhampton
> QLD 4701                              Tel: +61 (0)7 4923 8121
> Australia                             Fax: +61 (0)7 4923 8222
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor