Dear Jenny,

When i used  your code for treating the duplicates (spots are spotted more
than twice), it works fine and the results are as expected, but it gives
warning messages.

i have pasted the code below...

> MA.q <- normalizeBetweenArrays(MA.l, method="quantile")
> boxplot(MA.q$M~col(MA.q$M), names=colnames(MA.q$M))
> MA.q <- MA.q[order(MA.q$genes$ID),]
> x <- unique(MA.q$genes$ID)
> MA.q$genes$spotrep <- NULL
> for (i in 1:length(x)) {
+     y <- which( MA.q$genes$ID == x[i] )
+     MA.q$genes$spotrep[y] <- 1:length(y)
+     }
> MA.s <- MA.q[MA.q$genes$spotrep <= 2 , ]
> design <- c(1,1,-1,1,1)
> corfit <- duplicateCorrelation(MA.s, design, ndups=2, spacing=1)
*Warning messages:
1: Too much damping - convergence tolerance not achievable in: glmgam.fit(dx,
dy, start = start, tol = tol, maxit = maxit, trace = trace)
2: Too much damping - convergence tolerance not achievable in: glmgam.fit(dx,
dy, start = start, tol = tol, maxit = maxit, trace = trace)
3: Too much damping - convergence tolerance not achievable in: glmgam.fit(dx,
dy, start = start, tol = tol, maxit = maxit, trace = trace)
4: Too much damping - convergence tolerance not achievable in: glmgam.fit(dx,
dy, start = start, tol = tol, maxit = maxit, trace = trace)
*> corfit$consensus
[1] 0.5030145
> fit <- lmFit(MA.s, design, ndups=2, spacing=1,correlation=corfit$cor)
> fit.eb <- eBayes(fit)
> write.fit(fit.eb, file="data/1d.xls", adjust="BH")

I dont understand the message, is it ok....to carry on the analysis or do I
have alter the code. can you please kindly explain this?

Thanks for the help

with regards,
vinoy



-- 
Vinoy......

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