[BioC] Background correction - limma

Helen Cattan helen.cattan at jenner.ac.uk
Tue Apr 6 14:29:20 CEST 2004


I am trying to use backgroundCorrect - method = half or minimum but get
the following error:

> files=dir(pattern="*\\.gpr")
> RG=read.maimages(files, columns=list(Rf="F635 Median", Gf="F532
Median", Rb="B635 Median", Gb="B532 Median"))
> names(RG)
> RG$genes=readGAL()
> RG$printer=getLayout(RG$genes)
> samples=read.table("sampleinformationa.txt", header=TRUE, sep="\t",
> samples
> spottypes=readSpotTypes()
> RG$genes$Status=controlStatus(spottypes, RG)
> RG = backgroundCorrect(RG, method="minimum")
> MA=normalizeWithinArrays(RG, RG$printer)
> MA=normalizeBetweenArrays(MA)
> design=c(1,-1)
> cor=dupcor.series(MA$M,design,ndups=2)
Loading required package: nlme 
Loading required package: lattice 
Error in array(val[["varBeta"]], c(rnkm1, rnkm1), list(namCoef,
namCoef)) : 
        length of dimnames[1] not equal to array extent

Then I manually altered the background values of the genepix files so
after background subtraction the previously negative (F635/532-B635/532)
values were zero, omitted the backroundCorrect method and this worked
fine. However when I redid the alteration so after background
subtraction the previously negative values were 0.5, I got the same
error as above.

Has anyone any suggestions?


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