Error in Matrix
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rasii • 0
@rasii-10044
Last seen 5.2 years ago

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)

minfi methylation EPIC microarray illumina • 1.0k views
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Entering edit mode
@kasper-daniel-hansen-2979
Last seen 3 months ago
United States
Well, it looks like a bug. Could you start an issue on the Github page? On Sat, Apr 23, 2016 at 3:07 AM, rasii [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User rasii <https: support.bioconductor.org="" u="" 10044=""/> wrote Question: > Error in Matrix <https: support.bioconductor.org="" p="" 81199=""/>: > > 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) > > ------------------------------ > > Post tags: minfi, methylation, EPIC microarray, illumina > > You may reply via email or visit Error in Matrix >
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