[BioC] help w/ bg.correct.gcrma

[Jenny Drnevich]

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