Shame on me... The .CEL files were in the wrong directory... A lot of thanks for the quick response!
Sake On 4 feb, 17:15, Henrik Bengtsson <henrik.bengts...@aroma-project.org> wrote: > Skip Step 2, because getPath(csR) won't work when the data set is empty. > > /Henrik > > On Fri, Feb 4, 2011 at 8:00 AM, Henrik Bengtsson > > <henrik.bengts...@aroma-project.org> wrote: > > Hi. > > > The rather confusing error message actually implies that no data files > > where found in the data set directory. So: > > > 1. Make sure you have your CEL files in rawData/B&T/Mapping250K_Nsp/ > > > 2. Does print(list.files(path=getPath(csR)) list your CEL files? > > > 3. See troubleshooting page on 'Setup of directory structures': > > http://aroma-project.org/troubleshooting/DirectoryStructures > > > 4. Update aroma.affymetrix to v1.9.0, cf.http://aroma-project.org/install > > > 5. Try csR <- AffymetrixCelSet$byName(dataSetName, cdf=cdf, > > verbose=-10); It should show how many files it finds. > > > BTW, although > > > cdf <- AffymetrixCdfFile$byName(chipType); > > > happens to work (and not the cause of your problems), you should really use > > > cdf <- AffymetrixCdfFile$byChipType(chipType); > > > Let us know if any of these helped. > > > /Henrik > > > On Fri, Feb 4, 2011 at 6:16 AM, Sake van Pelt <tlep.nav.eka...@gmail.com> > > wrote: > >> Hi All, > > >> I´m encountering a problem with the following code: > > >>>library("aroma.affymetrix"); > >>>library("ACNE"); > >>>log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE); > > >>>setwd("D:/Users/Who Am I/Documents/0School/Jaar 5/BMCG/Array data/LUMC SNP > >>>250k nsp"); > > >>>dataSetName <- "B&T"; > >>>chipType <- "Mapping250K_Nsp"; > > >>>pairs <- matrix(c( > > >> "AR1000900A_N_241110_(Mapping250K_Nsp)_2.CEL","AR1000900B_N_241110_(Mapping250K_Nsp)_2.CEL", > > >> "AR1000901A_N_241110_(Mapping250K_Nsp).CEL","AR1000901B_N_241110_(Mapping250K_Nsp).CEL", > > >> "AR1000902A_N_241110_(Mapping250K_Nsp).CEL","AR1000902B_N_241110_(Mapping250K_Nsp).CEL", > > >> "AR1000903A_N_291110_(Mapping250K_Nsp).CEL","AR1000903B_N_241110_(Mapping250K_Nsp).CEL", > > >> "AR1000904A_N_241110_(Mapping250K_Nsp).CEL","AR1000904B_N_241110_(Mapping250K_Nsp).CEL" > >> ), ncol=2, byrow=TRUE); > >>>colnames(pairs) <- c("Tumor", "Bloed"); > > >>>cdf <- AffymetrixCdfFile$byName(chipType); > >>>csR <- AffymetrixCelSet$byName(dataSetName, cdf=cdf); > >>>print(csR); > > >> Error in list(`print(csR)` = <environment>, `print.Object(csR)` = > >> <environment>, : > > >> [2011-02-04 15:04:48] Exception: Argument 'x' is of length 1 although > >> the range ([0,0]) implies that is should be empty. > >> at throw(Exception(...)) > >> at throw.default(sprintf("Argument 'x' is of length %d although the > >> range ([%s,%s]) implies that is should be empty.", length(x), > >> range[1], range[2])) > >> at throw(sprintf("Argument 'x' is of length %d although the range > >> ([%s,%s]) implies that is should be empty.", length(x), range[1], > >> range[2])) > >> at getIndices.Arguments(static, ..., length = length) > >> at getIndices(static, ..., length = length) > >> at method(static, ...) > >> at Arguments$getIndex(idx, max = n) > >> at getFile.GenericDataFileSet(this, 1) > >> at getFile(this, 1) > >> at getUnitNamesFile.AffymetrixCelSet(this) > >> at getUnitNamesFile(this) > >> at getChipType.AffymetrixCelSet(this) > >> at getChipType(this) > >> at sprintf("Chip type: %s", getChipType(this)) > >> at as.character.AffymetrixCelSet(x) > >> at as.character(x) > >> at print(as.character(x)) > >> at print.Object(csR) > >> at print(csR) > > >>> sessionInfo() > >> R version 2.12.1 (2010-12-16) > >> Platform: x86_64-pc-mingw32/x64 (64-bit) > > >> locale: > >> [1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands. > >> 1252 LC_MONETARY=Dutch_Netherlands.1252 > >> LC_NUMERIC=C > >> [5] LC_TIME=Dutch_Netherlands.1252 > > >> attached base packages: > >> [1] stats graphics grDevices utils datasets methods > >> base > > >> other attached packages: > >> [1] ACNE_0.4.2 MASS_7.3-9 > >> aroma.affymetrix_1.7.0 aroma.apd_0.1.7 affxparser_1.20.0 > >> R.huge_0.2.0 aroma.core_1.7.0 > >> [8] aroma.light_1.16.1 matrixStats_0.2.2 > >> R.rsp_0.4.0 R.cache_0.3.0 R.filesets_0.9.0 > >> digest_0.4.2 R.utils_1.5.3 > >> [15] R.oo_1.7.4 R.methodsS3_1.2.1 > > >>> traceback() > >> 20: throw.Exception(Exception(...)) > >> 19: throw(Exception(...)) > >> 18: throw.default(sprintf("Argument 'x' is of length %d although the > >> range ([%s,%s]) implies that is should be empty.", > >> length(x), range[1], range[2])) > >> 17: throw(sprintf("Argument 'x' is of length %d although the range > >> ([%s,%s]) implies that is should be empty.", > >> length(x), range[1], range[2])) > >> 16: getIndices.Arguments(static, ..., length = length) > >> 15: getIndices(static, ..., length = length) > >> 14: method(static, ...) > >> 13: Arguments$getIndex(idx, max = n) > >> 12: getFile.GenericDataFileSet(this, 1) > >> 11: getFile(this, 1) > >> 10: getUnitNamesFile.AffymetrixCelSet(this) > >> 9: getUnitNamesFile(this) > >> 8: getChipType.AffymetrixCelSet(this) > >> 7: getChipType(this) > >> 6: sprintf("Chip type: %s", getChipType(this)) > >> 5: as.character.AffymetrixCelSet(x) > >> 4: as.character(x) > >> 3: print(as.character(x)) > >> 2: print.Object(csR) > >> 1: print(csR) > > >> All the .CEL files and the .cdf annotation file are in the right path > >> as described athttp://www.aroma-project.org/node/68and > >>http://aroma-project.org/node/66. > > >> -- > >> 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 websitehttp://www.aroma-project.org/. > >> To post to this group, send email to aroma-affymetrix@googlegroups.com > >> To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/ -- 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/
