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 at http://www.aroma-project.org/node/68 and >> 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 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/ >> > -- 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. 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