[BioC] Questions on getting information from affy's CEL, CDF or 1lq file s

Wang, Hui Hui_Wang at affymetrix.com
Wed Mar 12 09:28:19 MET 2003


I am exploring the affy packages and I have trouble to get information I
need (part is because I am not so farmilar with the language and the
package). I have the following questions, your help will be really

1)how to get the coordinates of each probe intensities? For example, in the
.CEL file, there is x, y and intensity columns corresponding to each probes.
I used read.celfile to read information. If there seems no way to get the x,
y columns which are the corrdinate of the probes (there is no method
provided from Class Cel). Are there other functions to use?  Similar
question to .CDF file. 

2). How to extract non-control, non-qc probe information?

3) for many of the functions listed under affy package, there is no help
file. For a simple example, read.affybatch, or write.celfile etc. are there
other place to look?


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