Hello, I am having some troubles with exporting my data from CEL files to B-allele Frequency Files and Log R Ratios. I have successfully installed the aroma packages, made the appropriate directories for annotationData and rawData, and so far there are some basic setting statements that work fine.
library('aroma.affymetrix') library("aroma.core") tags <- "ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY"; dataSet <- "AAML0531"; chipType <- "GenomeWideSNP_6"; # call annotation file cdf <- AffymetrixCdfFile$byChipType(chipType=chipType) csRone <- AffymetrixCelSet$byName(dataSet, cdf=cdf); This works fine.. Then I saw the export manual on the website, and following the http://www.aroma-project.org/howtos/writeDataFrame and I get the following error message when I try to set up the following. # set the workin directory and dataset ds <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags, chipType=chipType); Could you please help me resolving this issue? Thanks so much, Marijana Error message [2013-05-28 18:15:23] Exception: No such root path directories: at #09. findByName.GenericDataFileSet(static, name = name, tags = tags, chipType = chipType, ..., paths = paths, mustExist = TRUE, subdirs = "GenomeWideSNP_6") - findByName.GenericDataFileSet() is in environment 'R.filesets' at #08. NextMethod("findByName", subdirs = chipType) - NextMethod() is in environment 'base' at #07. findByName.AromaUnitSignalBinarySet(static, name = name, tags = tags, chipType = chipType, ..., paths = paths, mustExist = TRUE) - findByName.AromaUnitSignalBinarySet() is in environment 'aroma.core' at #06. findByName(static, name = name, tags = tags, chipType = chipType, ..., paths = paths, mustExist = TRUE) - findByName() is in environment 'R.filesets' at #05. withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning")) - withCallingHandlers() is in environment 'base' at #04. suppressWarnings({ path <- findByName(static, name = name, tags = tags, chipType = chipType, ..., paths = paths, mustExist = TRUE) }) - suppressWarnings() is in environment 'base' at #03. byName.AromaUnitTotalCnBinarySet(static, ...) - byName.AromaUnitTotalCnBinarySet() is in environment 'aroma.core' at #02. byName(static, ...) - byName() is in environment 'R.filesets' - originating from '<text>' at #01. AromaUnitTotalCnBinarySet$byName(dataSet, tags = tags, chipType = chipType) - AromaUnitTotalCnBinarySet$byName() is local of the calling function Error: No such root path directories: -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.