[BioC] Question on read.probematix

[James W. MacDonald]

Gunther Höning wrote:
>  Dear list,
> 
> I have a short question on read.probematrix().
> I use an Affymetrix hgu133plus2 chip. It has 1164 rows and 1164 columns.
> Thus I expect 1354896 (=1164*1164) messured intensity points. But reading a
> cel-file I receive 2 (pm and mm) * 604258 = 1208516 entries.
> The difference is 146380. Even if I take the QC into account I'm slightly
> confused.

If you look at the .tiff file in GCOS you will see that there is a 
'checkerboard' of probes that go completely around the outside of the 
chip. These are used by the affy software to align the scanner, and are 
scanned, but are neither QC nor expression measuring probes. I believe 
these make up most of your missing probes.

Best,

Jim


> 
> It would be kind if you helped me.
> 
> Greetings
> 
> Gunther
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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