[BioC] help w/ bg.correct.gcrma

[James MacDonald]

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 like
to 
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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