[BioC] re About ndups error chol(V)

[赵烨]

Dear Prof. Gorden:

Thank you very much for your help. I am sorry for not telling the
enough information. I have two two-colour arrays to analyze. Each
probe is present three times on each chip side by side. I use Genepix
to get the gps files.
Here is my session information and functions.

> sessionInfo()
R version 2.2.0, 2005-10-06, i386-pc-mingw32

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "base"

>library(limma)
>targets
>myfun<-function(x,threshold=50){
  okred<-abs(x[,"F635 Median"]-x[,"F635 Mean"])<threshold
  okgreen<-abs(x[,"F532 Median"]-x[,"F532 Mean"])<threshold
  as.numeric(okgreen & okred)
  }
>RG <- read.maimages(targets$Filename, source="genepix", wt.fun=myfun)
>RG$printer <- getLayout(RG$genes)
>RG <- backgroundCorrect(RG, method="normexp", offset=50)
>MA<-normalizeWithinArrays(RG,layout,method="loess")
>design<-c(1,1)
>library(statmod)
>cor <- duplicateCorrelation(MA,design,ndups=3)
>cor$consensus.correlation
>fit<-lmFit(MA,design,ndups=3,correlation=cor$consensus.correlation)

The consensus correlation returned by duplicateCorrelation is -0.5.
And when I input
"fit<-lmFit(MA,design,ndups=3,correlation=cor$consensus.correlation)"
,it complains an error on chol(V).

Questions:
(1) why this error comes out?
(2) If the cor$consensus.correlation value is negative, could I use
the function "fit<-lmFit()"?  If not, what is the range of the
cor$consensus.correlation that I can use in the function
"fit<-lmFit()".
(3) Do I or must I need swap the dyes for my experiment?
(4) Do I need use function "MA <- normalizeBetweenArrays(MA)" when I
use the function "fit<-lmFit()"?