[BioC] error in gcrma background correction

Raffaele Calogero raffaele.calogero at unito.it
Thu May 13 09:14:04 CEST 2004

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?

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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