Hi Vinoy,

I'm not exactly sure what the warning messages are, but it looks like there 
was trouble fitting the model for 4 of the genes. This is in the help page 
for 'duplicateCorrelation':

The function may take long time to execute as it fits a mixed linear model 
for each gene for an iterative algorithm. It is not uncommon for the 
function to return a small number of warning messages that correlation 
estimates cannot be computed for some individual genes. This is not a 
serious concern providing that there are only a few such warnings and the 
total number of genes is large. The consensus estimator computed by this 
function will not be materially affected by a small number of genes.

So, it's probably fine to carry on with the analysis. I wouldn't be 
surprised if you also get 4 error messages from 'lmFit', but again, it's 
only 4 genes that may have some wacky values...

Cheers,
Jenny


At 04:50 AM 1/5/2007, Vinoy Kumar Ramachandran wrote:
>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......

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich@uiuc.edu 
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