[BioC] bioconductor 1.7 and kooperberg

[Gordon K Smyth]

The data input for kooperberg() has been changed (greatly simplified).   The function now accepts
an RGList object.

Reading either the documentation help("kooperberg") or the limma changelog would have told you of
this change.

Gordon


> Date: Wed, 26 Oct 2005 17:28:40 US/Arizona
> From: scholz at Ag.arizona.edu
> Subject: [BioC] bioconductor 1.7 and kooperberg
> To: bioconductor at stat.math.ethz.ch
>
> R2.2
> 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?
>
> Thanks,
>
> Matt
>
> ---------------------------------------------
> College of Agriculture and Life Sciences Web Mail.
> http://ag.arizona.edu