[BioC] help w/ bg.correct.gcrma

[FCollin at genelogic.com]

There may be an easier way, but this worked for me as of last month - 
dunno if functions changed since. 

# Grp.AB is an Affybatch object 
Grp.pm.mtx <- pm(Grp.AB)
Grp.mm.mtx <- mm(Grp.AB)

Grp.GroupInfo <-getGroupInfo(Grp.AB)


Grp.pm.gcbgc.eb.mtx <- do.call("cbind", 
        lapply(X=1:ncol(Grp.pm.mtx), 
                       FUN=function(jj)    bg.adjust.gcrma( Data = 
array(c(Grp.pm.mtx[, jj], Grp.mm.mtx[, jj]), dim=c(nrow(Grp.pm.mtx), 2)),
                    gcgroup=Grp.GroupInfo,
                    estimate="eb",
                    triple.goal=F)))
 


-franncois




Jenny Drnevich <drnevich at uiuc.edu>
Sent by: bioconductor-bounces at stat.math.ethz.ch
10/31/03 01:19 PM

 
        To:     bioconductor at stat.math.ethz.ch
        cc: 
        Subject:        [BioC] help w/ bg.correct.gcrma


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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