[BioC] help w/ bg.correct.gcrma

[Zhijin Wu]

Thanks, James. I will update the "return" line in gcrma to be 
compatible with R-1.8.

Jean

----- Original Message -----
From: James MacDonald <jmacdon at med.umich.edu>
Date: Friday, October 31, 2003 9:17 pm
Subject: Re: [BioC] help w/ bg.correct.gcrma

> The first try should read like this:
> 
> bgaffy 
> <-
> bg.correct.gcrma(rawaffy,gcgroup=getGroupInfo
(rawaffy),estimate="eb",triple.goal=TRUE)
> 
> Note the error in your message. You can also set 
> triple.goal=FALSE, but
> you have to do one or the other.
> 
> As for the multi-argument returns message, that is simply a change 
> as of
> R-1.8.0 that really only concerns the package maintainer. For now the
> functions will work fine (except for the annoying warnings).
> 
> HTH,
> 
> Jim
> 
> 
> 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> >>> Jenny Drnevich <drnevich at uiuc.edu> 10/31/03 16:29 PM >>>
> Hi,
> 
> I want to explore the GC-based background correction in gcrma. I'd 
> liketo 
> get the bg corrected PM values, not the summary values. I think I 
> can do
> 
> this with bg.correct.gcrma, but I'm having problems getting it to 
> run 
> correctly. I'm looking at some of the Affy spike-in data, and 
> running R 
> 1.8.0 and Bioconductor 1.3. I followed the format I found from 
> ?bg.correct.gcrma:
> 
> > bgaffy 
> <-
> bg.correct.gcrma(rawaffy,gcgroup=getGroupInfo(rawaffy),estimate="eb")
Loading required package: hgu95aprobe
> Loading required package: matchprobes
> Error in FUN(array(newX[, i], d.call, dn.call), ...) :
>         Argument "triple.goal" is missing, with no default
> In addition: Warning messages:
> 1: multi-argument returns are deprecated in: return(y = yhat, wt)
> 2: multi-argument returns are deprecated in: return(y = yhat, wt)
> 3: multi-argument returns are deprecated in: return(y = yhat, wt)
> 4: multi-argument returns are deprecated in: return(y = yhat, wt)
> 5: multi-argument returns are deprecated in: return(y = yhat, wt)
> 
> Additionally, I tried:
> 
> bgaffy
> <-
> bg.correct.gcrma(rawaffy,gcgroup=getGroupInfo(rawaffy),estimate="mle")
> and got over 50 of the "multi-argument returns" warning messages. Any
> ideas 
> about what I need to do?
> 
> Thanks,
> Jenny
> 
> 
> Jenny Drnevich, Ph.D.
> Department of Animal Biology
> 515 Morrill Hall
> 505 S Goodwin Ave
> Urbana, IL 61801
> USA
> 
> ph: 217-244-6826
> fax: 217-244-4565
> e-mail: drnevich at uiuc.edu
> 
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