[BioC] a just.gcrma question

[Zhijin (Jean) Wu]

The affinity.info will be computed using probe sequence of your array
type, but the function that maps probe sequence to probe affinity is
trained on a non-specific binding experiment on hgu95av2 platform.

WHen type is not specified, "fullmodel" is used (both probe sequence and
MM measurements are used to estimate background).

best,
Jean

On Tue, 2 May 2006, Jianping Jin wrote:

> 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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