reading with lumi
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Ed Siefker ▴ 230
@ed-siefker-5136
Last seen 4 months ago
United States
I am trying to read Level 1 methylation data from the TCGA into bioconductor. The platform is HumanMethylation27, which is supported by lumi, right? Here is my R session: > library(lumi) Loading required package: methylumi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation("pkgname")'. Loading required package: nleqslv KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 Attaching package: ?lumi? The following object(s) are masked from ?package:methylumi?: estimateM, getHistory Warning message: found methods to import for function ?as.list? but not the generic itself > > fileName <- 'jhu-usc.edu_COAD.HumanMethylation27.1.lvl-1.TCGA- AA-3555-01A-01D-0820-05.txt' > example.lumi <- lumiR(fileName) Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds >
lumi lumi • 1.1k views
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