[BioC] Wow, what have I done

[Loren Engrav]

Well I guess not done

So I have the justGCRMA object "Gibran81"

And try

> QCReport(Gibran81,file="AffyQCReportGibran81.pdf")

And get back

Error in box(...) : invalid 'which' specification
In addition: Warning messages:
1: In plot.window(...) : "which" is not a graphical parameter
2: In plot.xy(xy, type, ...) : "which" is not a graphical parameter
3: In axis(side = side, at = at, labels = labels, ...) :
  "which" is not a graphical parameter
4: In axis(side = side, at = at, labels = labels, ...) :
  "which" is not a graphical parameter

Maybe I am out of my league

Funny, a few months ago I did 60 chips and mixed linear regression worked
just fine

Loren Engrav
Univ Washington
Seattl




> From: Loren Engrav <engrav at u.washington.edu>
> Date: Sat, 08 Dec 2007 15:19:01 -0800
> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Conversation: [BioC] Wow, what have I done
> Subject: Re: [BioC] Wow, what have I done
> 
> 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
> 
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