[BioC] Importing CDF file for custom array using makecdfenv

[Michal Okoniewski]

 Hi Ann, 

This is what I used to do:

library(makecdfenv)
library(altcdfenvs)
library(simpleaffy)

raw.data <- read.affy()
tmp.env=make.cdf.env("XXX.cdf")
my.env2 <- wrapCdfEnvAffy(tmp.env, 712, 712, "myenv") #change 712 into
291 in your case my.env2 at envName <-"HGU133a my environment"
my.env <- as(my.env2,"environment")
raw.data.mt at cdfName <- "my.env" 

or alternatively, and probably better: create the metadata package gzip
file with make.cdf.package (setting the name and path), install it with
R CMD INSTALL and just do:

library(packagename) #not sure it this is necessary 
raw.data at cdfName <- "packagename"

Cheers,
Michal 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Ann Hess
Sent: 23 August 2006 22:16
To: BioConductor Mail List
Subject: [BioC] Importing CDF file for custom array using makecdfenv

I have CEL (and CDF) files from a custom Affy chip and I need to import
the CDF file into BioConductor.  I am using R 2.3.1, Bioconductor 1.8
and Windows XP.

I have read the makecdfenv vignette and other postings about this
process, but I can't figure out how to make it work!  I have the
original CDF file in the same directory as my CEL files.  I have
downloaded ActivePerl and the R source package installation files as
suggested in the makecdfenv vignette (although I don't understand how
these are used).

After loading affy and reading in the CEL files (into an affybatch
object called "data"), I used the following
commands:
library(makecdfenv)
make.cdf.package("XXX.cdf",species="XXX")
XXXcdf=make.cdf.env("XXX.cdf")

I do not get any errors, but when I try to look at the affybatch object
I get the following message:

Error in getCdfInfo(object) : Could not obtain CDF environment, problems
encountered:
Specified environment does not contain XXX Library - package XXXcdf not
installed Data for package affy did not contain XXXcdf Bioconductor -
XXXcdf not available AffyBatch object size of arrays=291x291 features
(15887 kb) cdf=XXX (??? affyids) number of samples=24 Error in
getCdfInfo(object) : Could not obtain CDF environment, problems
encountered:
Specified environment does not contain XXX

I have tried putting the CDF file (created by BioC) in the R libraries
folder with other libraries, but no luck.

In the makecdfenv vignette it says to "open a terminal with an operating
system shell and write R CMD INSTALL XXXcdf", but I don't know how to do
this on windows.

Any suggestions would be greatly appreciated!

Ann

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