[BioC] a just.gcrma question

[Jianping Jin]

Thanks a lot Jim!
JP-

--On Tuesday, May 02, 2006 10:51 AM -0400 "James W. MacDonald" 
<jmacdon at med.umich.edu> wrote:

> Hi Jianping,
>
> 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?
>
> The affinities are calculated based on the MM sequences, which are
> extracted from the corresponding probe package. Since they are based on
> the sequence of the probes, there is no reason to use an individual data
> set.
>
> You _could_ compute the affinities for a particular chip and then save
> that data somewhere so you wouldn't have to compute it every time you ran
> gcrma, which is why you have the option of specifying the affinity.info.
> In fact it was suggested at one time by Robert Gentleman that we should
> put the affinity.info somewhere (I suggested the probe packages) so it
> wouldn't have to be recomputed every time, which is simply a waste of
> compute cycles. However, people got busy and it never got implemented.
>
>>
>> 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?
>
> There _is_ a default parameter. Any time you see something like
>
> type = c("fullmodel", "affinities", "mm", "constant")
>
> in the arguments of a function, there should be a corresponding
>
> type <- match.arg(type)
>
> in the body of the function. If you don't specify a type, then the
> argument that will be matched by default is the first one in the argument
> vector, which in this case is 'fullmodel'.
>
> HTH,
>
> Jim
>
>
>>
>> I will appreciate it if you could help me out!
>>
>> Jianping
>>
>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>> 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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>>
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>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
>
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xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
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
x Fax: (919)843-3103            x
x E-mail: jjin at email.unc.edu    x
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx