[BioC] Affy mas5calls on Hu6800 arrays

Stronach, Euan A e.stronach at imperial.ac.uk
Wed Nov 10 17:57:07 CET 2004

Dear All,

I'm looking at some older affy data from the Hu6800 arrays. In the Affy
package I'm normalising by either mas5 or by RMA which is working fine.
However when I try to generate P/M/A calls by:


I get the following output and error message:

Getting probe level data...
Computing p-values
Making P/M/A Calls
Error in if (y < alpha1) { : missing value where TRUE/FALSE needed

I have done the same type of treatment on U95 arrays and it works

Any ideas as to why the Hu6800 chips are causing a problem? And more
importantly, any idea of how to get it working or of an alternative way
to generate P/M/A calls? Most of the data I want to look at is of this
format so any help would be very gratefully received.



p.s. I am very much of the "newbie" category wrt R so if you can keep it
simple that would be great!

(R 2.0.0 on windows xp with default Bioconductor packages installed)

Euan Stronach, PhD
Research Associate
Section of Molecular Therapeutics
Department of Cancer Medicine

Imperial College London
7th Floor Laboratories
MRC Cyclotron Building
Du Cane Road
London W12 ONN

E-mail: e.stronach at imperial.ac.uk
Mobile: +44 (0)7762 900661
Office/Lab: +44 (0)208 3838 345
Fax: +44 (0)208 3838 349

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