[R] Question on bioconductor: reading affymetrix data

Pintilie, Melania Melania.Pintilie at uhn.on.ca
Mon Oct 25 22:53:39 CEST 2004

Hi everyone,

My purpose is to read a .CEL file into R.

The .CEL file was created from a .CAB by using DTT software found on
Affymetrix website 
I read the .CEL file in R using ReadAffy as follows:
> d2=ReadAffy(widget=T)
and I complete the fields as required.
It does not complain. For example I could find the description:
> description(d2)
Experimenter name: BB 
Laboratory: FFL 
Contact information: 
Title: Heter 
URL: www.bioconductor.org 

A 1 word abstract is available. Use 'abstract' method.

Information is available on: samples, preprocessing 

But if I want to see the values for MM I get an error:

> mm(d2)[1:2]
Note: You did not specify a download type.  Using a default value of: Win32 
This will be fine for almost all users
Error in if ((is.null(deps)) || (length(deps) == 0) || (deps == ""))
return(NULL) : 
        missing value where TRUE/FALSE needed

I appreciate any ideas you may have. Thank you.

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