[BioC] justGCRMA: Argument is missing, with no default

James MacDonald jmacdon at med.umich.edu
Thu Apr 8 14:53:20 CEST 2004

Your call to optimize.by is wrong. Instead of optimize.by=c(,"memory")
use optimize.by="memory".



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> Dick Beyer <dbeyer at u.washington.edu> 04/07/04 07:56PM >>>
I am trying to use juastGCRMA, but am running into a problem part way
through the calculation:

mydata.gcrma <- justGCRMA(filenames=rownames(pData(pd.heart)),
phenoData=pd.heart, optimize.by=c(,"memory"), type = c("fullmodel"))
Computing affinities..Done.
Error in all(arg == choices) : Argument is missing, with no default

The one argument I did not specify was "compress".  I have a mix of
both compressed and uncompressed files.  (ReadAffy handles that case.)

I did try this with only uncompressed files, but still got the same
error message.  I am running on windows 2000, with R 1.9.0 beta 3/27

base 1.9.0 
utils 1.9.0 
graphics 1.9.0 
stats 1.9.0 
methods 1.9.0 
gcrma 1.0.6 
affy 1.4.21 
Biobase 1.4.10 
tools 1.9.0 
splines 1.9.0 
matchprobes 1.0.2 
mgu74av2cdf 1.4.3 
mgu74av2probe 1.0 

I'd greatly appreciate any help or suggestions.

Thanks very much,
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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