[BioC] RE: altcdfenvs error

[Wu, Xiwei]

The problem was solved after upgrading to the newest development version of
altcdfenvs (version 1.1-11). However, I found that I need to use envsccdf
instead of sccdf to make it work, unlike what is described in the vignettes.


Envsccdf <- as(sccdf, "environment")
abatch at cdfName <- "sccdf" #boxplot(abatch) does not work
abatch at cdfName <- "envsccdf" #boxplot(abatch) works

Xiwei
-----Original Message-----
From: Wu, Xiwei 
Sent: Thursday, March 24, 2005 10:11 AM
To: 'bioconductor at stat.math.ethz.ch'
Subject: altcdfenvs error

I was trying to build a cdfEnvAffy object from yeast2cdf following the
documentation of Alternative CDF environment for 2(or more)-genomes chips. I
got the following error. Am I missing sth here?

> yeastcdf <- wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf")
> print(yeastcdf)
Instance of class CdfEnvAffy:
 name     : yeast2cdf 
 chip-type: yeast2cdf 
 size     : 496 x 496 
 10928 probe set(s) defined.
> ids <- geneNames(yeastcdf)
> ids.yeast<- scan(file="Y_IDs.txt", what="")
Read 5814 items
> sccdf <- yeastcdf[ids.yeast]
> print(sccdf)
Instance of class CdfEnvAffy:
 name     : yeast2cdf-subset 
 chip-type: yeast2cdf 
 size     : 496 x 496 
 5814 probe set(s) defined.
> envsccdf <- as(sccdf, "environment")
> raw at cdfName <- "sccdf"
> boxplot(raw)
Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : 
        Invalid object for as.environment
> raw at cdfName
[1] "sccdf"
> getCdfEnvAffy(raw)
Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) : 
        Invalid object for as.environment
> class(sccdf)
[1] "CdfEnvAffy"
attr(,"package")
[1] "altcdfenvs"

> raw at cdfName <- "envsccdf"
> class(envsccdf)
[1] "environment"
> boxplot(raw)
Error in ans[[i]][, i.probes] : incorrect number of dimensions

Any help will be highly appreicated.

Xiwei Wu, MD, PhD
Assistant Research Scientist
Department of Biomedical Informatics
Beckman Research Insitute
City of Hope National Medical Center
Duarte, CA 91010
Phone: (626) 359-8111 ext. 65071

"EMF <COH.org>" made the following annotations.
------------------------------------------------------------------------------
SECURITY/CONFIDENTIALITY WARNING:  This message and any atta...{{dropped}}