Hi. On Sat, Jul 3, 2010 at 2:22 AM, larryns <larr...@gmail.com> wrote: > Okay I managed to debug the problem. It seemed that indexOf didn't > like my filenames because the files had parentheses in the name.
Your troubleshooting is correct, and yes, related issues have been reported before; Thread 'ArrayExplorer problem', started 2010-01-26: http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/749f2fa7ef1d398d/d33e1d528bf4377c?lnk=gst&q=Cannot+read+CEL+file+header#d33e1d528bf4377c Thread 'ArrayExplorer: Error in readCelHeader(pathname) Options', started 2010-05-14: http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/38ade690dffd1ee/825288ef8cd5cfef?lnk=gst&q=Cannot+read+CEL+file+header#825288ef8cd5cfef indexOf() uses regular expression pattern matching internally, and there parentheses have a special meaning. This should be fixed in the next release of aroma.core (and R.filesets). In the meanwhile, as explained in http://aroma-project.org/howtos/updateOrPatch, you can patch it by: library("aroma.affymetrix"); downloadPackagePatch("R.filesets"); downloadPackagePatch("aroma.core"); downloadPackagePatch("aroma.affymetrix"); Let me know if this helps. > But > now display(ae) fails because the path for the html file is messed up, > with backslashes ("\") instead of forward slashes ("/"). I don't understand if this is because you tried your own workaround, or if it is because of the bug, or what. But, please install the patch and retry. You might want to clear out the correspond reports/ directory. Hope it helps Henrik > > Any thoughts on this? > > Thanks, > -Larry. > > On Jul 2, 3:21 am, larryns <larr...@gmail.com> wrote: >> Hi, >> >> I've seen a post with this error before, but I haven't encountered a >> solution. Here is my simple script: >> >> library(aroma.affymetrix) >> >> verbose <- Arguments$getVerbose(-8, timestamp=T) >> >> # Load the annotation files >> chipType <- "MoEx-1_0-st-v1" >> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="core") >> cs <- AffymetrixCelSet$byName("MNSMA", cdf=cdf) >> >> # background normalization >> bc <- RmaBackgroundCorrection(cs) >> rma <- process(bc, verbose=verbose) >> >> # quantile normalization >> qn <- QuantileNormalization(rma, typesToUpdate="pm") >> print(qn) >> csN <- process(qn, verbose=verbose) >> >> # summarize by exon >> #plmEx <- ExonRmaPlm(csN, mergeGroups=F) >> #fit(plmEx, verbose=verbose) >> >> # summarize by probeset >> plm <- RmaPlm(csN) >> fit(plm, verbose=verbose) >> >> rs <- calculateResiduals(plm, verbose=verbose) >> ae <- ArrayExplorer(rs) >> setColorMaps(ae, c("log2,log2neg,rainbow", "log2,log2pos,rainbow")) >> process(ae, interleaved="auto", verbose=verbose) >> >> --- >> The relevant, screendump: >> >> > process(ae, interleaved="auto", verbose=verbose) >> >> 20100702 03:19:33|Generating ArrayExplorer report... >> 20100702 03:19:33| Setting up ArrayExplorer report files... >> 20100702 03:19:33| Copying template files... >> 20100702 03:19:33| Source path: /Library/Frameworks/R.framework/ >> Resources/library/aroma.core/reports/includes >> 20100702 03:19:33| Destination path: reports/includes >> 20100702 03:19:33| Copying template files...done >> 20100702 03:19:33| Setting up ArrayExplorer report files...done >> 20100702 03:19:33| Updating ArrayExplorer.onChipType.js... >> 20100702 03:19:33| Source: /Library/Frameworks/R.framework/Resources/ >> library/aroma.core/reports/templates/rsp/ArrayExplorer/ >> ArrayExplorer.onChipType.js.rsp >> 20100702 03:19:33| Output path: reports/MNSMA/RBC,QN,RMA >> 20100702 03:19:33| Compiling RSP... >> 20100702 03:19:33| Color maps: log2,log2neg,rainbow, >> log2,log2pos,rainbow >> 20100702 03:19:33| Chip type: MoEx-1_0-st-v1,core >> Error in readCelHeader(pathname) : >> Cannot read CEL file header. File not found: NA/NA >> In addition: Warning messages: >> 1: In min(x) : no non-missing arguments to min; returning Inf >> 2: In max(x) : no non-missing arguments to max; returning -Inf >> 20100702 03:19:33| Compiling RSP...done >> 20100702 03:19:33| Updating ArrayExplorer.onChipType.js...done >> 20100702 03:19:33|Generating ArrayExplorer report...done> traceback() >> >> 34: stop("Cannot read CEL file header. File not found: ", filename) >> 33: readCelHeader(pathname) >> 32: getHeader.AffymetrixCelFile(this) >> 31: getHeader(this) >> 30: getCdf.AffymetrixCelFile(this$files[[1]], ...) >> 29: getCdf(this$files[[1]], ...) >> 28: getCdf.AffymetrixCelSet(this) >> 27: getCdf(this) >> 26: clearCache.AffymetrixCelSet(res) >> 25: NextMethod(generic = "clearCache", object = this, ...) >> 24: clearCache.ResidualSet(res) >> 23: clearCache(res) >> 22: extract.GenericDataFileSet(X[[1L]], ...) >> 21: FUN(X[[1L]], ...) >> 20: lapply.default(dsList, FUN = extract, files, ...) >> 19: lapply(dsList, FUN = extract, files, ...) >> 18: extract.GenericDataFileSetList(this, ..., onDuplicated = "error") >> 17: extract(this, ..., onDuplicated = "error") >> 16: getFileList.GenericDataFileSetList(this, ii, ...) >> 15: getFileList(this, ii, ...) >> 14: getFullNames.AromaMicroarrayDataSetTuple(setTuple) >> 13: getFullNames(setTuple) >> 12: eval(expr, envir, enclos) >> 11: eval(rExpr, envir = envir) >> 10: sourceRsp.default(file = pathname, response = response, ...) >> 9: sourceRsp(file = pathname, response = response, ...) >> 8: rspToHtml.default(pathname, path = NULL, outFile = outFile, outPath >> = outPath, >> overwrite = TRUE, envir = env) >> 7: rspToHtml(pathname, path = NULL, outFile = outFile, outPath = >> outPath, >> overwrite = TRUE, envir = env) >> 6: updateOnChipTypeJS.ArrayExplorer(this, ...) >> 5: updateOnChipTypeJS(this, ...) >> 4: setup.ArrayExplorer(this, ..., verbose = less(verbose)) >> 3: setup(this, ..., verbose = less(verbose)) >> 2: process.ArrayExplorer(ae, interleaved = "auto", verbose = verbose) >> 1: process(ae, interleaved = "auto", verbose = verbose)> sessionInfo() >> >> R version 2.11.1 (2010-05-31) >> x86_64-apple-darwin9.8.0 >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] preprocessCore_1.10.0 Biobase_2.8.0 >> aroma.affymetrix_1.6.0 >> [4] aroma.apd_0.1.7 affxparser_1.20.0 >> R.huge_0.2.0 >> [7] aroma.core_1.6.0 aroma.light_1.16.0 >> matrixStats_0.2.1 >> [10] R.rsp_0.3.6 R.cache_0.3.0 >> R.filesets_0.8.2 >> [13] digest_0.4.2 R.utils_1.4.2 >> R.oo_1.7.3 >> [16] affy_1.26.1 R.methodsS3_1.2.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.16.0 tools_2.11.1 >> Warning message: >> 'DESCRIPTION' file has 'Encoding' field and re-encoding is not >> possible >> >> --- >> >> From some (really) preliminary debugging, it looks like getPathname is >> failing because this.$pathname is NA. So I think the pathnames aren't >> being stored? If someone could please shed some light on this issue, >> I'd be very grateful. >> >> Thanks for any help, >> -Larry. > > -- > 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. 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/
