Hi Bioc, There seems to be a Windows-specific memory allocation error when running makeGenomicRatioSetFromMatrix() from within DMRcate::DMR.plot() calling the IlluminaHumanMethylationEPICanno.ilm10b4.hg19 annotation . You can find the offending error in the most recent build here: http://bioconductor.org/checkResults/3.9/bioc-LATEST/DMRcate/tokay2-checksrc.html
> DMR.plot(ranges=results.ranges, dmr=1, CpGs=myBetas, phen.col=cols, > genome="hg19", samps=samps) Loading required package: IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Failed with error: 'cannot allocate vector of size 510.7 Mb' Error in makeGenomicRatioSetFromMatrix(CpGs, array = "IlluminaHumanMethylationEPIC", : cannot load annotation package IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Calls: DMR.plot -> makeGenomicRatioSetFromMatrix Execution halted Can the minfi developers investigate this please? The purpose of calling makeGenomicRatioSetFromMatrix() is to access the chromosome position and ID from a methylation matrix with probe IDs as rownames. DMR.plot() also needs the beta values so I am killing 2 birds with 1 stone with this call. Best, Tim -- =================== Tim Peters, PhD Bioinformatics Research Officer | Immunogenomics Laboratory | Immunology Division Garvan Institute of Medical Research 384 Victoria St., Darlinghurst, NSW, Australia 2010 E: t.pet...@garvan.org.au<mailto:t.pet...@garvan.org.au> | W: http://www.garvan.org.au | P: +612 9295 8325 NOTICE Please consider the environment before printing this email. This message and any attachments are intended for the addressee named and may contain legally privileged/confidential/copyright information. If you are not the intended recipient, you should not read, use, disclose, copy or distribute this communication. If you have received this message in error please notify us at once by return email and then delete both messages. We accept no liability for the distribution of viruses or similar in electronic communications. This notice should not be removed. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
