I have DNA methylation data that I have collected from male and female subjects using the Illumina 450K Array platform.  I have read the data into R as a "methyLumiSet" from .IDAT files using the "methyLumi" package and I am planning on pre-processing the data using some of the normalization functions in the "wateRmelon" package:

suppressPackageStartupMessages(require(methylumi))
suppressPackageStartupMessages(require(wateRmelon))
suppressPackageStartupMessages(require(IlluminaHumanMethylation450kanno.ilmn12.hg19))

# Read sample data. 
# phenoData is a data.frame with the row names = SentrixPosition_barcode 
# and columns containing sample group, age and gender. 
# Barcodes are pulled from a column in phenoData called 'barcodes'.

phenoData <- read.csv("/Users/Martens/Desktop/08272014/IDATs/Sample_Sheet.csv",header=TRUE) 
barcodes <- subset(phenoData, select=barcodes)

# Import .IDAT files as methyLumiSet
methyLumiSet <- methylumIDAT(barcodes = barcodes, pdat = phenoData,
idatPath = "/Users/Martens/Desktop/08272014/IDATs")

As confirmation that all of the features were imported, I checked the number of rows in methyLumiSet:

nrow(methyLumiSet)
Features
    485577

The methyLumiSet is based off of the eSet class in Biobase.  I would like to remove all features spanning X and Y chromosomes, as is common practice in DNA methylation analysis.  

As an initial attempt, I tried to determine which probes fall on the Y chromosome using the following code with the idea that I would then remove those probes from the methyLumiSet.

methyLumiSet.ChrY <- methyLumiSet[fData(methyLumiSet)$CHROMOSOME=="Y", ]

however, when I check the number of probes, the result is 0 features:

nrow(methyLumiSet.ChrY)
Features
    0

I cannot figure out why I am unable to subset features of my methyLumiSet.  However, a potential issue might be with the annotation.  When I try to run the methyLumi function 'featureFilter' to remove the X chromosome, I get the following error messages:

methyLumiSet.Xfilt <- featureFilter(methyLumiSet, exclude.ChrX = TRUE)

Warning message:
In .featureFilter(eset, require.entrez = require.entrez, require.GOBP =            
require.GOBP,  : HumanMethylation450k probes annotate to multiple accessions(!)
 Error in mget(featureNames(eset), envir = annotate::getAnnMap("CHR", annChip),  : 
 error in evaluating the argument 'envir' in selecting a method for     function 'mget': 
 Error: getAnnMap: package IlluminaHumanMethylation450k not available

When I try to install IlluminaHumanMethylation450k, I get the following:

source("http://bioconductor.org/biocLite.R")
biocLite("IlluminaHumanMethylation450k")

BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.3), R version 3.2.0.
Installing package(s) ‘IlluminaHumanMethylation450k’
Old packages: 'stringi', 'VariantAnnotation'
Update all/some/none? [a/s/n]: 

I type 'a' to update all and after updating I get the following error message.

# Warning message: package ‘IlluminaHumanMethylation450k’ is not available (for R version 3.2.0) 

My only guess is that my issue with subsetting probes by chromosome has to do with not being able to load the annotation information, but I am stuck on trying to figure out how to fix it.  According to the reference manual for methyLumi, the package should be compatible with R version 3.2.0 and depends on IlluminaHumanMethylation450kanno.ilmn12.hg19 but even when I require this package I don't understand how to link the annotation data to the methyLumiSet.

any advice on properly annotating a methyLumiSet and/or removing X,Y chromosomes from a methyLumiSet would be great.  I am pretty new to R.

I would prefer to do this without coercing to another structure (e.g., SummarizedExperiment/minfi type of object) if possible.  Thanks!

-Chris

Using the example for methylumiR() (since there isn't a runnable example for methylumIDAT() and I don't feel like rummaging around for some IDAT files), I get this:

> example(methylumiR)

mthylR> ## Read in sample information
mthylR> samps <- read.table(system.file("extdata/samples.txt",
mthylR+                                 package = "methylumi"),sep="\t",header=TRUE)

mthylR> ## Perform the actual data reading
mthylR> ## This is an example of reading data from an
mthylR> ## Sentrix Array format file (actually two files,
mthylR> ## one for data and one for QC probes)
mthylR> mldat <- methylumiR(system.file('extdata/exampledata.samples.txt',package='methylumi'),
mthylR+                     qcfile=system.file('extdata/exampledata.controls.txt',package="methylumi"),
mthylR+                     sampleDescriptions=samps)

mthylR> mldat

Object Information:
MethyLumiSet (storageMode: lockedEnvironment)
assayData: 1536 features, 10 samples
  element names: Avg_NBEADS, BEAD_STDERR, betas, methylated, pvals, unmethylated
protocolData: none
phenoData
  sampleNames: M_1 M_2 ... F_10 (10 total)
  varLabels: sampleID SampleLabel Sample Gender
  varMetadata: labelDescription
featureData
  featureNames: AATK_E63_R AATK_P519_R ... ZP3_P220_F (1536 total)
  fvarLabels: TargetID ProbeID ... PRODUCT (17 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
Major Operation History:
            submitted            finished
1 2015-06-22 14:13:20 2015-06-22 14:13:20
                                                                                                                                                                                                            command
1 methylumiR(filename = system.file("extdata/exampledata.samples.txt",     package = "methylumi"), qcfile = system.file("extdata/exampledata.controls.txt",     package = "methylumi"), sampleDescriptions = samps)

And we can see what chromosomes are being measured:

> table(fData(mldat)$CHROM)

  1  10  11  12  13  14  15  16  17  18  19   2  20  21  22   3   4   5   6   7
122  46 113  77  26  37  62  41  76  36  75  89  36  23  25  89  66  70  98 122
  8   9   X
 58  62  87

Which may be why you are having problems filtering on ChrY.