This was reported a while ago by Dan Tenenbaum, forgotten about by me and fixed tonight in minfi v1.13.2
The previous use of the read.450k.exp function, where there was both a base = SOMETHING and a targets object (created by read.450k.sheet) with a targets$Basename with values like SOMETHING/SOMETHINGELSE is no longer support (it used to be that the base argument was ignored). User now just have to do sheet = read.450k.sheet(ARGS) rgset = read.450k.exp(targets = sheet) We now support giving a base argument in case targets$Basename does not contain the full path. And this time I hope it works.... Best, Kasper On Tue, Nov 18, 2014 at 7:38 PM, Jovana Maksimovic < jovana.maksimo...@mcri.edu.au> wrote: > Hi, > At present, the minfi 1.13.1 read.450k.exp function can result in an > erroneous file path when reading in IDAT files using a targets file. > The following line of code can create a path where "base" is repeated as > "targets$Basename" already contains "base" if read.450k.sheet was used to > create "targets": > > files <- file.path(base, targets$Basename) > > This results in an error when trying to read in the files: > rgSet <- read.450k(files, extended = extended, verbose = verbose) > > This is an example of the error: > Error: processing vignette 'minfi.Rnw' failed with diagnostics: > chunk 7 (label = paths) > Error in read.450k(files, extended = extended, verbose = verbose) : > The following specified files do not > exist:/home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata//home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata/5723646052/5723646052_R02C02_Grn.idat, > /home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata//home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata/5723646052/5723646052_R04C01_Grn.idat, > /home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata//home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata/5723646052/5723646052_R05C02_Grn.idat, > /home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata//home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata/5723646053/5723646053_R04C02_Grn.idat, > /home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata//home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata/5723646053/5723646053_R05C02_Grn.idat, > /home/biocbuild/bbs-3.1-bioc/R > Execution halted > > This is currently affecting the development version of minfi and any other > packages that are using minfi functions to read in methylation data. > Regards, > Jovana Maksimovic > > > > > ______________________________________________________________________ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > ______________________________________________________________________ > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
