[BioC] limma - dupcor.series

[Gordon Smyth]

At 01:59 AM 16/04/2004, Helen Cattan wrote:
>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)

No need to type 'RG$printer', the function will find it automatically.

> > 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

I don't know what the problem is, presumably it is a problem with 
method="minimum". Can you please type summary(MAmin2$M), 
summary(MAmin2$weights) and summary(cor$cor.genes) to give more information?

> > 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

The warnings are no problem.

Gordon