Dear Bioconductor users,

When I use VanillaICE package to estimate LOH with hidden Markov models
I get an error message (below)- I was wandering if you can use 

this package with SNP 6.0 affymetrix platform.

Thank you!
Best,

Sergii

 

> class(crlmmResults)

[1] "SnpCnvCallSetPlus"

attr(,"package")

[1] "oligoClasses"

 

 

> chr1.calls <- as(crlmmResults, "HmmSnpCallSet")

> stateNames(chr1.calls) <- c("loss", "ret")

> pCHOM(chr1.calls) <- c(0.999, 0.7)

> initialStateProbability(chr1.calls) <- c(1 - 0.99, 0.99)

> predictions(chr1.calls) <- matrix(NA,
nrow(chr1.calls),ncol(chr1.calls))

> chr1.calls <- hmm(chr1.calls) #### SEGMENTATION

 

chr1 <- sample.snpset[chromosome(sample.snpset) == "1", 1]

graph.par <- getPar(chr1, use.chromosome.size=TRUE)

plotSnp(graph.par, chr1)

[1] "71312 out of 71312 predictions are NA."

Error in plot.default(0:1, type = "n", xlim = op$xlim[i, ], ylim =
op$predictions.ylim,  : 

  subscript out of bounds


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