[BioC] a just.gcrma question

[jjin at email.unc.edu]

Hi Jean,

Thanks for your very clear explanation!

best whishes,

JP-

Quoting "Zhijin (Jean) Wu" <zwu at alexander.stat.brown.edu>:

> 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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>