Hi, I am following the example for low level analysis for Human Exon arrays:
http://www.aroma-project.org/node/37 I downloaded all the appropriate cdf files from: http://www.aroma-project.org/chipTypes/MoEx-1_0-st-v1 All the commands in the Vignette work fine until fit() chipType <- "MoEx-1_0-st-v1" cdf <- AffymetrixCdfFile$byChipType(chipType, tags="fullR1,A20080718,MR") print(cdf) getPathname(cdf) cs <- AffymetrixCelSet$byName("HevnerMouseEx_10.11.16", cdf=cdf) setCdf(cs,cdf) bc <- RmaBackgroundCorrection(cs, tag="fullR1") csBC <- process(bc,verbose=verbose) qn <- QuantileNormalization(csBC, typesToUpdate="pm") print(qn) csN <- process(qn, verbose=verbose) plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE) print(plmTr) plmEx <- ExonRmaPlm(csN, mergeGroups=FALSE) print(plmEx) fit(plmTr, verbose=verbose) Fitting model of class ExonRmaPlm... ExonRmaPlm: Data set: HevnerMouseEx_10.11.16 Chip type: MoEx-1_0-st-v1,fullR1,A20080718,MR Input tags: fullR1,QN Output tags: fullR1,QN,RMA,merged Parameters: (probeModel: chr "pm"; shift: num 0; flavor: chr "affyPLM"; treatNAsAs: chr "weights"; mergeGroups: logi TRUE). Path: plmData/HevnerMouseEx_10.11.16,fullR1,QN,RMA,merged/MoEx-1_0-st-v1 RAM: 0.00MB Identifying non-estimated units... Writes CDF header and unit names... Writes CDF header and unit names...done Writes QC units... Units left: 0 Writes QC units...done Writes 11415 units... Units left: 10415, 9415, 8415, 7415, 6415, 5415, 4415, 3415, 2415, 1415, 415, 0 Writes 11415 units...done <snip> Writes 11415 units... Units left: 10415, 9415, 8415, 7415, 6415, 5415, 4415, 3415, 2415, 1415, 415, 0 Writes 11415 units...done Writes 2963 units... Units left: 1963, 963, 0 Writes 2963 units...done Error in list(`fit(plmTr, verbose = verbose)` = <environment>, `fit.ProbeLevelModel(plmTr, verbose = verbose)` = <environment>, : [2010-11-17 14:40:04] Exception: Failed to create a valid mono-cell CDF: The cell indices are not contiguous: 1, -913715, 0, 21002, -21002, 31326208, -31326207, 31326207, -31326208, 739252, -738296, 31812, -32768, 913720, -913719, -1, 955, 244737, -245692, -31325951, -257, 19196744, -19196744, 745944, -744988, 913727, -913726, 752636, -751680, 913734, -913733, 759328, -758372, 913741, -913740, 766020, -765064, 913748, -913747, 772712, -772709, 244733, -244736, 5036, -5036, 2873, -2873, 3 at throw(Exception(...)) at throw.default("Failed to create a valid mono-cell CDF: The cell indices are not contiguous: ", paste(udcells, collapse = ", ")) at throw("Failed to create a valid mono-cell CDF: The cell indices are not contiguous: ", paste(udcells, collapse = ", ")) at createMonocellCdf.AffymetrixCdfFile(this, ..., verbose = less(verbose)) at createMonocellCdf(this, ..., verbose = less(verbose)) at getMonocellCdf.AffymetrixCdfFile(cdf, ..., verbose = less(verbose)) Identifying non-estimated units...done Fitting model of class ExonRmaPlm...done > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] preprocessCore_1.12.0 affyio_1.18.0 Biobase_2.10.0 aroma.affymetrix_1.8.0 aroma.apd_0.1.7 affxparser_1.22.0 [7] R.huge_0.2.0 aroma.core_1.8.0 aroma.light_1.18.2 matrixStats_0.2.2 R.rsp_0.4.0 R.cache_0.3.0 [13] R.filesets_0.9.0 digest_0.4.2 R.utils_1.5.7 R.oo_1.7.4 affy_1.28.0 R.methodsS3_1.2.1 I just rev'ed to 2.12.0 and updated packages(). If anyone had a suggestion I would be very grateful. Thanks very much, Dick ******************************************************************************* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/members_fc_bioinfo.html http://staff.washington.edu/~dbeyer <http://staff.washington.edu/%7Edbeyer> ******************************************************************************* -- 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/
