Hi Paul, 

I am trying to follow the your "Read single channel GenePix in limma "
version of code  for my data.

I could able to run properly till "VSN normalization" but after that
when  I am running the duplicateCorrelation I am getting warnings.

 

 

These are the sequences of steps that I did starting normalization.

 

 

 

mat <- vsnMatrix(RG.final$G)

bb <- as.matrix(mat)

rownames(bb) <- RG.final$genes$Name

bb <- bb[order(rownames(bb)), ]

corfit <- duplicateCorrelation(bb, design, ndups=4)

There were 50 or more warnings (use warnings() to see the first 50)

Warnings are : 50: In sqrt(dfitted.values) : NaNs produced

 

So can you please help me out in this regard.

 

Thanks

Ashwin 

 



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