Hi all,
I am analysing the new Illumina EPIC methylation array and I keep getting the following error. Can anyone help me figure what/where I've gone wrong. Below is the code I have used:
>require(minfi)
>targets <- read.metharray.sheet(baseDir)
> RGset <- read.metharray.exp(targets = targets)
> RGset@annotation = c(array = "IlluminaHumanMethylationEPIC", annotation = "ilm10b2.hg19")
>RGset
RGChannelSet (storageMode: lockedEnvironment)
assayData: 1052641 features, 8 samples
element names: Green, Red
An object of class 'AnnotatedDataFrame'
sampleNames: 1 2 ... 134 (134 total)
varLabels: Sample_Name Sample_Group ... Basename (9
total)
varMetadata: labelDescription
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b2.hg19
>pd <- pData(RGset)
> densityPlot(RGset, sampGroups = pd$Sample_Group,
+ main = "Beta", xlab = "Beta")
Error in matrix(NA_real_, ncol = ncol(rgSet), nrow = length(locusNames), :
length of 'dimnames' [2] not equal to array extent
> densityBeanPlot(RGset, sampGroups = pd$Sample_Group)
Error in matrix(NA_real_, ncol = ncol(rgSet), nrow = length(locusNames), :
length of 'dimnames' [2] not equal to array extent
> raw <- preprocessRaw(RGset)
Error in matrix(NA_real_, ncol = ncol(rgSet), nrow = length(locusNames), :
length of 'dimnames' [2] not equal to array extent
I cant seem to be able to plot anything and it doesnt even let me process the data. What am I doing wrong? help please..
Rasi
P.S Im using the latest version of R (beta) and minfi (1.17.10)
