Dear BioC,

We have our own customized Affy chip. I got my CEL files and related CDF file. Based on the book "The Analysis of Gene Expression Data" by editors Parmigiani et al., I put all the files under the working dir, and evoke the function ReadAffy(). After that, I tried to use hist() or boxplot(), I got the following error message:

Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered:
Specified environment does not contain Cxxxxx500001
Library - package cxxxxx500001cdf not installed
Data for package affy did not contain cxxxx500001cdf

Also tried read.celfile() and read.cdffile(), but those methods were not recognized. I guess, over the time, the package Affy has been modified.

Now, my question is: how am I going to read in the CDF file? Since it is our own chip, I have nether package cxxxx500001cdf nor package Cxxxx50001probe. Should I create my own packages? If so, how to do that? 


Thanks a million!
Johnny

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