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

Dick Beyer dbeyer at u.washington.edu
Thu Apr 8 01:56:23 CEST 2004

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 build.

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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