[BioC] trouble using GCRMA

[Zhijin (Jean) Wu]

Thanks Jim.
With the older package xy2indices did not take cdf as an argument. Wong 
and I both had the older version. It is not a bug with the current 
version.

Jean


On Fri, 15 Jun 2007, James W. MacDonald wrote:

> 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 I am betting you have an outdated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
>>
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>
>
> -- 
> 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
>
>
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