[R] Error in var(x, na.rm = na.rm) : no complete element pairs

[ml-r-help at epigenomics.com]

Carlos Morales wrote:
> Hello,
> 
> I still have the same error which I have written in the Subject field, I leave here the code and I hope you can help me with this:
> 
[removed]

the lengthy code example does not make it easier to help you, in particular without the
data you used. All the commented out code should have been removed before posting.
My guess is that you use R < 2.8.0 and generate a vector s which contains only NAs.
Try to inspect your function filter.clones by putting a browser()
call somewhere before the sd() call and run it again.
See ?browser and ?trace.

And you could vectorize this (and other parts), e.g.
the last loop would be rewritten as

tripliclones.info$Estandar_desviation <- apply(tripliclones.info[ ,2:4], 1, function(x)
sd(as.numeric(x), na.rm=TRUE))

Regards, Matthias


R version 2.7.1 (2008-06-23)
> b <- rep(NA,4)
> sd(b)
Error in var(x, na.rm = na.rm) : missing observations in cov/cor
> sd(b, TRUE)
Error in var(x, na.rm = na.rm) : no complete element pairs


R version 2.8.1 (2008-12-22)
> b<- rep(NA,4)
> sd(b)
[1] NA
> sd(b, TRUE)
[1] NA

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Matthias Burger                     Project Manager/ Biostatistician
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