[BioC] a just.gcrma question

[James W. MacDonald]

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
> 
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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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