[BioC] rma error on 48 mgu74av2 slides

[James MacDonald]

Which development version of affy? There was a devel version in the recent past that was broken and would give this error. The most current version (1.2.15) works for me, so you might try updating.

You can also check to see if there actually are missing values in your AffyBatch. pm(peter48.raw)[is.na(pm(peter48.raw))] However, if there are missing values there must be something broken.

Jim



James W. MacDonald
UMCCC Microarray Core Facility
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> Dick Beyer <dbeyer at u.washington.edu> 05/02/03 05:41PM >>>
I got the following error from rma

>peter48.raw <- ReadAffy(widget=TRUE)
>peter48.raw <- rma(peter48.raw)
Background correcting
Error in density(x, kernel = "epanechnikov", n = 2^14) : 
        x contains missing values

This is for 48 mgu74av2 mouse chips.

Any suggestions for pinpointing the problem, I would greatly appreciate.

windows 2000, R 1.6.2, Bioconductor development release. Dual Xeon 2.8GHz box with 4Gb RAM.

Thanks much,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
			Seattle, WA 98105-6099

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