[BioC] bioconductor 1.7 and kooperberg

scholz@Ag.arizona.edu scholz at Ag.arizona.edu
Wed Oct 26 17:28:40 CEST 2005

Bioconductor 1.7 
Windows XP

Hi all,

I was happily using the kooperberg function for background correction until I
upgraded to 1.7. Using the same input (cut and pasted from the same document to
avoid typos), I get an error in 1.7 that I don't get when using 1.6 and R2.1.1.
Here's the relevant input/output:

> targetsB <- readTargets("targetsB.txt")
> spottypes <- readSpotTypes()

#I define a function called filters here, but have left it out for brevity

> RGB <- read.maimages(targetsB$FileName, source="genepix", wt.fun=filters)
Read B115_R480_G430.gpr 
Read B116_R480_G430.gpr 
Read B117_R480_G430.gpr 
Read B118_R480_G430.gpr 
Read B119_R480_G430.gpr 
Read B120_R480_G430.gpr 
Read B121_R480_G430.gpr 
Read B122_R480_G430.gpr 
Read B123_R480_G430.gpr 
Read B124_R480_G430.gpr 
Read B125_R480_G430.gpr 
Read B126_R480_G430.gpr 
> RGBgenes <- readGAL("MOB-1-3.anno.gal")
> RGBlayout <- getLayout(RGBgenes)
> read.series(targetsB$FileName, suffix=NULL, skip=31, sep="\t", quote="\"") 
[1] "12 slides read"
> RGBmodel <- kooperberg(targetsB$FileName, layout=RGBlayout)
Error in kooperberg(targetsB$FileName, layout = RGBlayout) : 
Data missing from RG$other: re-run read.maimages with
 other=c("F635 SD","B635 SD","F532 SD","B532 SD","B532 Mean","B635 Mean","F
Pixels","B Pixels", "Block")
In addition: Warning message:
Coercing LHS to a list 

Any ideas?



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