[BioC] trouble using GCRMA

[James W. MacDonald]

wong wrote:
> Hi all,
> I just started to work with gcrma to get expression indices for
> microarrays of yeast 2.0.
> The error occured when I tried to make expression summary with package gcrma.
> Some of the R code and error information are showed below:
> 
> 
>>Data<-ReadAffy()
>>est<-gcrma(Data)
> 
> Adjusting for optical
> effect................................................Done.
> Computing affinities.Error in xy2indices(p$x, p$y, cdf = cdfpackagename) :
>         unused argument(s) (cdf = "yeast2cdf")
> 
> 
> I'm using R-2.5.0-win32 and gcrma_2.8.1. I guess I am doing something
> wrong here but I do not realize what.
> Any help would be appreciate

What do you get from sessionInfo()? I am betting you have an outdated 
affy package (indicating that you did not use biocLite() to install things).

Best,

Jim


> 
> 
> wong
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.