[BioC] a just.gcrma question

[Jianping Jin]

Dear list:

There is an issue that is not clear to me, even after I read "Description 
of gcrma package" and the on-line help. The default setting for 
"affinity.info" is NULL. Based on the description for the program it 
appears that NULL does not use apm (for PM probe), amm (MM probe), or index 
of your own data. Are the affinities calculated in just.gcrma based on 
"hgu95av2" data set or something else with affinity.info=NULL?

Another question I have is for "type". As there is no default parameter for 
the type setting, which model does "just.gcrma" take for running without 
defining any parameters?

I will appreciate it if you could help me out!

Jianping

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x Jianping Jin Ph.D.            x
x Bioinformatics scientist      x
x Center for bioinformatics     x
x 3133 Bioinformatics Building  x
x CB# 7104                      x
x University of North Carolina  x
x Chapel Hill, NC 27599         x
x Tel: (919)843-6105            x
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x E-mail: jjin at email.unc.edu    x
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