[BioC] Wow, what have I done

[Loren Engrav]

Ok
But R.app does not show justGCRMA package
But via google I find it in gcrma
So I do
> Gibran81  <-  justGCRMA() #81 .cel files
And voila I get

Computing affinities.Done.
Adjusting for optical
effect......................................................................
............Done.
Adjusting for non-specific
binding.....................................................................
............Done.
Normalizing
Calculating Expression
> objects()
[1] "Gibran81"              "affinity.spline.coefs"

It did take 25" but then what is 25"?
And
justGCRMA(..., filenames=character(0),
  widget=getOption("BioC")$affy$use.widgets,
  compress=getOption("BioC")$affy$compress.cel,
  celfile.path=getwd(),
  sampleNames=NULL,
  phenoData=NULL,
  description=NULL,
  notes="",
  normalize=TRUE, 
  bgversion=2, affinity.info=NULL,
  type=c("fullmodel","affinities","mm","constant"),
  k=6*fast+0.5*(1-fast), stretch=1.15*fast+1*(1-fast),
  correction=1, rho=0.7, optical.correct=TRUE,
  verbose=TRUE, fast=TRUE, minimum=1, optimize.by = c("speed","memory"),
  cdfname = NULL, read.verbose = FALSE)
Is rather scary, especially k

But assuming "default" is Ok, it is finished, I have gcrma of 81 .cel files,
thank you very much

Also please see new thread in R-Mac on R.app ?bug, thank you

Loren Engrav
Univ Washington
Seattle





From: Sean Davis <sdavis2 at mail.nih.gov>
Date: Sat, 8 Dec 2007 13:26:23 -0500
To: Loren Engrav <engrav at u.washington.edu>
Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
Subject: Re: [BioC] Wow, what have I done



On Dec 8, 2007 11:36 AM, Loren Engrav <engrav at u.washington.edu> wrote:
> 
> And most of our previous stuff is gcrma and not sure mixing is a good idea
> if this is mixing

You might look at justGCRMA(), the GCRMA.

Sean