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

[Dick Beyer]

Hi Jim,

Thank you for pointing out my obvious syntax mistake.  I used the correct syntax and all worked well.  48 mgu74av2 chips, a mix of compressed and uncompressed, took about 5 minutes.

Sorry to have bothered you and everyone with such a trivial problem.

Thanks very much for your help,
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
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
*******************************************************************************

On Thu, 8 Apr 2004, James MacDonald wrote:

> Your call to optimize.by is wrong. Instead of optimize.by=c(,"memory")
> use optimize.by="memory".
> 
> Best,
> 
> Jim
> 
> 
> 
> 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 
> >>> 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
> 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,
> 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
> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html 
> 
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