Hello,
I am trying to convert a MethyLumiSet I have received into an RGChannelSet to use some minfi functions. I have read in the methylumi vignette that this should be possible as long as the OOB probes are included in the MethyLumiSet (http://bioconductor.org/packages/release/bioc/vignettes/methylumi/inst/doc/methylumi450k.pdf, page 9).
So, following the vignette, I tried this:
myRGSet <- as(myMethyLumiSet, "RGChannelSet")
Which led to the following error:
Fetching coordinates for hg19...
Error in getPlatform(chip) :
You need to specify either HM27 or HM450 as platform to run
But I am unsure how I should specify the platform, and if this is possible for EPIC in addition to 27K and 450K arrays. Is it? If not, is there any other way of converting a MethyLumiSet into an RGChannelSet?
Best wishes, Nala
sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server 7.6 (Maipo)
Matrix products: default BLAS: /mnt/254b78b9-76b4-422d-84b1-cc632bff60f7/Software/install/R-3.6.1/lib64/R/lib/libRblas.so LAPACK: /mnt/254b78b9-76b4-422d-84b1-cc632bff60f7/Software/install/R-3.6.1/lib64/R/lib/libRlapack.so
locale:
[1] LCCTYPE=enGB.UTF-8 LCNUMERIC=C LCTIME=enGB.UTF-8 LCCOLLATE=enGB.UTF-8
[5] LCMONETARY=enGB.UTF-8 LCMESSAGES=enGB.UTF-8 LCPAPER=enGB.UTF-8 LCNAME=C
[9] LCADDRESS=C LCTELEPHONE=C LCMEASUREMENT=enGB.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] affy1.62.0 methylumi2.30.0 FDb.InfiniumMethylation.hg192.2.0
[4] org.Hs.eg.db3.8.2 TxDb.Hsapiens.UCSC.hg19.knownGene3.2.2 GenomicFeatures1.36.4
[7] AnnotationDbi1.46.1 ggplot23.2.1 reshape21.4.3
[10] scales1.0.0 minfi1.30.0 bumphunter1.26.0
[13] locfit1.5-9.1 iterators1.0.12 foreach1.4.7
[16] Biostrings2.52.0 XVector0.24.0 SummarizedExperiment1.14.1
[19] DelayedArray0.10.0 BiocParallel1.18.1 matrixStats0.54.0
[22] Biobase2.44.0 GenomicRanges1.36.0 GenomeInfoDb1.20.0
[25] IRanges2.18.2 S4Vectors0.22.0 BiocGenerics_0.30.0
loaded via a namespace (and not attached):
[1] nlme3.1-140 bitops1.0-6 bit640.9-7 RColorBrewer1.1-2
[5] progress1.2.2 httr1.4.1 tools3.6.1 doRNG1.7.1
[9] nor1mix1.3-0 affyio1.54.0 R62.4.0 HDF5Array1.12.2
[13] lazyeval0.2.2 colorspace1.4-1 DBI1.0.0 withr2.1.2
[17] tidyselect0.2.5 prettyunits1.0.2 base642.0 bit1.1-14
[21] compiler3.6.1 preprocessCore1.46.0 xml21.2.2 pkgmaker0.27
[25] rtracklayer1.44.3 readr1.3.1 genefilter1.66.0 quadprog1.5-7
[29] askpass1.1 stringr1.4.0 digest0.6.20 Rsamtools2.0.0
[33] illuminaio0.26.0 siggenes1.58.0 GEOquery2.52.0 pkgconfig2.0.2
[37] scrime1.3.5 bibtex0.4.2 limma3.40.6 rlang0.4.5
[41] rstudioapi0.10 RSQLite2.1.2 DelayedMatrixStats1.6.0 mclust5.4.5
[45] dplyr0.8.3 RCurl1.95-4.12 magrittr1.5 GenomeInfoDbData1.2.1
[49] Matrix1.2-17 munsell0.5.0 Rcpp1.0.2 Rhdf5lib1.6.0
[53] lifecycle0.2.0 stringi1.4.3 MASS7.3-51.4 zlibbioc1.30.0
[57] rhdf52.28.0 plyr1.8.4 grid3.6.1 blob1.2.0
[61] crayon1.3.4 lattice0.20-38 splines3.6.1 multtest2.40.0
[65] annotate1.62.0 hms0.5.3 beanplot1.2 pillar1.4.2
[69] rngtools1.4 codetools0.2-16 biomaRt2.40.4 XML3.98-1.20
[73] glue1.3.1 BiocManager1.30.4 data.table1.12.8 vctrs0.2.4
[77] gtable0.3.0 tidyr1.0.2 purrr0.3.3 openssl1.4.1
[81] reshape0.8.8 assertthat0.2.1 xtable1.8-4 survival2.44-1.1
[85] tibble2.1.3 GenomicAlignments1.20.1 registry0.5-1 memoise1.1.0
ugh, yeah that'd require an EPIC mapping. it ought not to be particularly difficult, but honestly I'd suggest just reloading the IDAT files into minfi -- it will be less trouble and label swaps will be easier to catch. Plus then you'll have all of the raw data to work with.
Hi Tim,
Thank you very much for your answer. For some reason, I never got notified about your reply and thought my question went unsanswered. I am sorry about that.
I asked the question because in this case, I had only received the data in a MethyLumiSet and I do not have access to the IDATs. The transfer of only the MethyLumiSet took several days and was not very stable, so receiving the IDATs will be hard. In the end I found a workaround by writing my own code for what I had wanted to do with the RGChannelSet, but if there is an easier way, I would still be interested in knowing :-)
Best wishes, Nala