Dear list

I’m trying to convert a MethyLumi object into a GenoSet object, but when I try the following command I got an error:

> methyGenoSet <- MethyLumiM2GenoSet(filt, lib="IlluminaHumanMethylation27k.db")
Error in `rownames<-`(`*tmp*`, value = c("cg00000292", "cg00002426", "cg00003994",  :
  attempt to set 'rownames' on an object with no dimensions

This is the code I’m using to generate the MethyLumi object

sampledata <- read.table(file="sampledata_2round.txt", header=T, sep="\t")
barcodes <- as.character(sampledata$barcodes)
mset.raw <- methylumIDAT(barcodes)
sampleNames(mset.raw) <- sampledata$Sample_name
metadata <- read.table(file="metadata1.txt", header=T, sep="\t", row.names=1)

#Removing sample 061268N
mset.raw <- mset.raw[, -1]
metadata <- metadata[-1, ]
pData(mset.raw) <- metadata

#Transforming MethyLumi objet in MehyLumiM object
mset.lumi <- as(mset.raw, 'MethyLumiM')
##Perform quantile color balance adjustment
lumiMethy.c.adj <- lumiMethyC(mset.lumi)

##Perform ssn normalization
lumiMethy.c.ssn <- lumiMethyN(lumiMethy.c.adj, method="ssn")

##Filtering sex chromosome probes
load("adf.27k.rda")
XYs <- subset(adf.27k, Chr=="X" | Chr=="Y")
XYs <- as.character(XYs$Illumin_ID)
#Filtering just sex chromosome probes
XY <- subset(adf.27k, Chr != "X" & Chr != "Y")
XYs <- XY$Illumin_ID
lumiMethy.c.ssn <- lumiMethy.c.ssn[XYs,]

#Filtering probes based on IQR and cutoff = 0.1
filt <- nsFilter(lumiMethy.c.ssn, require.entrez=F, remove.dupEntrez=F, var.func=IQR, var.cutoff=0.1)$eset

And my sessionInfo()

R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] parallel  grid      stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] IlluminaHumanMethylation450k.db_2.0.7 FDb.InfiniumMethylation.hg19_2.0.10   BSgenome.Hsapiens.UCSC.hg19_1.3.19    BSgenome_1.28.0
 [5] Biostrings_2.28.0                     GenomicFeatures_1.12.3                plyr_1.8                              pheatmap_0.7.7
 [9] genefilter_1.42.0                     multtest_2.18.0                       annotate_1.38.0                       GOstats_2.26.0
[13] graph_1.38.3                          Category_2.26.0                       IlluminaHumanMethylation27k.db_1.4.7  limma_3.16.6
[17] lumi_2.14.0                           methylumi_2.8.0                       matrixStats_0.8.5                     ggplot2_0.9.3.1
[21] reshape2_1.2.2                        scales_0.2.3                          methyAnalysis_1.4.0                   org.Hs.eg.db_2.9.0
[25] RSQLite_0.11.4                        DBI_0.2-7                             AnnotationDbi_1.22.6                  Biobase_2.20.1
[29] GenomicRanges_1.12.4                  IRanges_1.20.2                        BiocGenerics_0.8.0

loaded via a namespace (and not attached):
 [1] affy_1.38.1           affyio_1.28.0         AnnotationForge_1.2.2 base64_1.1            beanplot_1.1          BiocInstaller_1.10.3  biomaRt_2.16.0
 [8] biovizBase_1.8.1      bitops_1.0-6          bumphunter_1.2.0      cluster_1.14.4        codetools_0.2-8       colorspace_1.2-2      dichromat_2.0-0
[15] digest_0.6.3          doRNG_1.5.5           foreach_1.4.1         genoset_1.14.0        GO.db_2.9.0           GSEABase_1.22.0       gtable_0.1.2
[22] Gviz_1.6.0            Hmisc_3.12-2          illuminaio_0.4.0      iterators_1.0.6       itertools_0.1-1       KernSmooth_2.23-10    labeling_0.2
[29] lattice_0.20-23       latticeExtra_0.6-26   locfit_1.5-9.1        MASS_7.3-29           Matrix_1.0-14         mclust_4.2            mgcv_1.7-26
[36] minfi_1.8.3           munsell_0.4.2         nleqslv_2.0           nlme_3.1-111          nor1mix_1.1-4         pkgmaker_0.17.4       preprocessCore_1.22.0
[43] proto_0.3-10          R.methodsS3_1.4.4     RBGL_1.36.2           RColorBrewer_1.0-5    RCurl_1.95-4.1        registry_0.2          reshape_0.8.4
[50] rngtools_1.2.3        rpart_4.1-3           Rsamtools_1.12.3      rtracklayer_1.20.4    siggenes_1.36.0       splines_3.0.2         stats4_3.0.2
[57] stringr_0.6.2         survival_2.37-4       tools_3.0.2           XML_3.95-0.2          xtable_1.7-1          XVector_0.2.0         zlibbioc_1.6.0

Thanks

Juan

-----
Dr. Juan Fernandez-Tajes
McCarthy's Group
The Wellcome Trust Centre for Human Genetics
University of Oxford
Jfertaj@well.ox.ac.uk<mailto:Jfertaj@well.ox.ac.uk>
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