[BioC] error in gcrma background correction

[Raffaele Calogero]

Hi ,
I am traying to calculare the intensity measure for the U133A 
latinsquare experiment from affymetrix.
I am using R 1.8.1 with gcrma  version 1.0.0 on linux RedHat 9.0 P4 2.6 
GHz, 1Gb Ram
I used the following commands:
 > library(affy)
 > library(gcrma)
 > data<-ReadAffy()
 > data.invariant.gcrma<-gcrma(data, normalize.method="invariantset")

and I got the following error and warnings:

Loading required package: hgu133atagprobe
Loading required package: matchprobes
background correction: gcrma
normalization: invariantset
PM/MM correction : pmonly
expression values: medianpolish
background correcting...Error in if (!(lo <- min(hi, IQR(x)/1.34))) (lo 
<- hi) || (lo <- abs(x[1])) ||  :
        missing value where TRUE/FALSE needed
In addition: There were 50 or more warnings (use warnings() to see the 
first 50)
Warning messages:
1: multi-argument returns are deprecated in: return(y = yhat, wt)
..
50: multi-argument returns are deprecated in: return(y = yhat, wt)

Does any body have any suggestion on how to get through this error message?
Which is the meaning of the warning messages?
Raf

-- 
Prof. Raffaele A. Calogero
Genomics and Bioinformatics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705410
Lab.   ++39 0116705408
Fax    ++39 0119038639
e-fax  ++39 0112365410
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
www:   www.bioinformatica.unito.it


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