[BioC] variable "ygs98cdfSYMBOL" was not found

Tomas Radivoyevitch radivot at hal.EPBI.cwru.edu
Thu Mar 24 16:07:27 CET 2005

It's been several years since I worked with yeast data, but I do recall a 
file called something like alias.txt from a stanford site which had lists of 
all the symbols for yeast genes.  Many genes had many different symbols 
associated with it, so it wasn't much fun.  Perhaps someone can comment on 
whether or not a set of unique yeast gene symbols has since then been agreed 
upon, i.e. to allow 1-to-1 mappings between gene symbols and ORFs.


----- Original Message ----- 
From: "John Zhang" <jzhang at jimmy.harvard.edu>
To: <shawnh at stanford.edu>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Thursday, March 24, 2005 9:47 AM
Subject: Re: [BioC] variable "ygs98cdfSYMBOL" was not found

> There is no annotation for SYMBOL in any of the annotation packages for 
> yeast
> because there were no source data available for SYMBOL when the packages 
> were
> built.
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>>    I'm new to bioconductor and am trying to use the simpleaffy package.
>>My example is simple:
>> >library(simpleaffy)
>> >library(ygs98cdf)
>> > x <-read.affy()
>> > x.rma<-call.exprs(x,"rma")
>>Background correcting
>>Calculating Expression
>> > pw<-pairwise.comparison(x.rma,"treatment",c("n","a"))
>> > pw.filtered<-pairwise.filter(pw)
>> > summary<-results.summary(pw.filtered,'ygs98cdf')
>>Error in get(x, envir, mode, inherits) : variable "ygs98cdfSYMBOL" was
>>not found
>>Any ideas?
>>Apologies if this is the wrong list for this mail.
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
> Jianhua Zhang
> Department of Medical Oncology
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
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