Hi, I suspect that you have an incomplete CDF file, e.g. due to downloading errors. Verify that you get the same output as the following:
> print(cdf); AffymetrixCdfFile: Path: annotationData/chipTypes/MoEx-1_0-st-v1 Filename: MoEx-1_0-st-v1,fullR1,A20080718,MR.cdf Filesize: 176.32MB Chip type: MoEx-1_0-st-v1,fullR1,A20080718,MR RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2560x2560 Number of cells: 6553600 Number of units: 265508 Cells per unit: 24.68 Number of QC units: 1 Especially the following: > print(getFileSize(cdf)); [1] 184886673 > print(getChecksum(cdf)); [1] "462897c4c2703764e075c945118f8c1a" > stopifnot(getChecksum(cdf) == "462897c4c2703764e075c945118f8c1a"); > If that is not the case, download the file again. Then continue with the following, which is what is happening internally when you get the error message: > cdfM <- getMonocellCdf(cdf, verbose=-5); Retrieving monocell CDF... Monocell chip type: MoEx-1_0-st-v1,fullR1,A20080718,MR,monocell Locating monocell CDF... Pathname: Locating monocell CDF...done Could not locate monocell CDF. Will create one for chip type... Creating monocell CDF... Chip type: MoEx-1_0-st-v1,fullR1,A20080718,MR Output pathname (temporary): annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0 -st-v1,fullR1,A20080718,MR,monocell.CDF.tmp Number of cells per group field: 1 Reading CDF group names... [...] Creating monocell CDF...done Could not locate monocell CDF. Will create one for chip type...done Retrieving monocell CDF...done > If you get this far without errors, things will work. Before restarting the analysis (your script), you need to delete all previous intermediate results, that is all subdirectories in probeData/ and plmData/ with names starting with HevnerMouseEx_10.11.16. Also, just in case, clear the memoization cache as follows: > library("R.utils"); > path <- file.path(getCacheRootPath(), "aroma.affymetrix", "MoEx-1_0-st-v1"); > unlink(path.expand(path), recursive=TRUE); /Henrik On Wed, Nov 17, 2010 at 4:33 PM, Richard Beyer <rpbe...@gmail.com> wrote: > 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 > ******************************************************************************* > > -- > 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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