[BioC] limma - dupcor.series

[Helen Cattan]

Hi,
 
-using Bioconductor v1.8.1 and limma v1.6.1
When I use backgroundCorrect(minimum) and then dupcor.series I don't get
a correlation value (NaN), if I don't use the backgroundCorrect method I
get a value but with a warning message. Does anyone have any suggestions
as to what is happening here and how I can sort it out please? (I
realize the experimental design is hopeless but I have to work with what
I'm given). I don't have any missing/blank values but obviously have
negative values after background subtraction. Code and warning are given
below.
Thanks,
 
Helen
 
> files=dir(pattern="*\\.gpr")
> RG=read.maimages(files, columns=list(Rf="F635 Median", Gf="F532
Median", Rb="B635 Median", Gb="B532 Median"), wt.fun=wtflags(0))
> names(RG)
> RG$genes=readGAL()
> RG$printer=getLayout(RG$genes)
> samples=read.table("sampleinformationa.txt", header=TRUE, sep="\t",
as.is=TRUE)
> samples
> spottypes=readSpotTypes()
> RG$genes$Status=controlStatus(spottypes, RG)
> RGmin=backgroundCorrect(RG, method="minimum")
> MAmin=normalizeWithinArrays(RGmin, RG$printer)
> MAmin2=normalizeBetweenArrays(MAmin)
> design=c(1,1,1,1)
> cor=dupcor.series(MAmin2$M, design, ndups=2, spacing=1)
Loading required package: statmod 
 
Attaching package 'statmod':
 
 
        The following object(s) are masked from package:limma :
 
         matvec vecmat 
 
> cor$cor
[1] NaN
> MAdef=normalizeWithinArrays(RG, RG$printer)
> MAdef2=normalizeBetweenArrays(MAdef)
> design=c(1,1,1,1)
> cor=dupcor.series(MAdef2$M, design, ndups=2, spacing=1)
Warning messages: 
1: Too much damping - convergence tolerance not achievable in:
glmgam.fit(dx, dy, start = start, tol = tol, maxit = maxit, trace =
trace) 
2: Too much damping - convergence tolerance not achievable in:
glmgam.fit(dx, dy, start = start, tol = tol, maxit = maxit, trace =
trace) 
3: Too much damping - convergence tolerance not achievable in:
glmgam.fit(dx, dy, start = start, tol = tol, maxit = maxit, trace =
trace) 
[1] 0.7891024
 

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