[BioC] Affy array layout

Nathan.Watson-Haigh at csiro.au Nathan.Watson-Haigh at csiro.au
Fri Jul 18 06:56:59 CEST 2008

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?


Dr. Nathan S. Watson-Haigh        (publish under Haigh, N.S.)
OCE Post Doctoral Fellow
CSIRO Livestock Industries
J M Rendel Laboratory 
QLD 4701                              Tel: +61 (0)7 4923 8121
Australia                             Fax: +61 (0)7 4923 8222

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