Hi, could you please forward your UGP file to me; I think I know what the problem is, but I guess it easier for me to check it myself first.
BTW, although this looks like a custom CDF - if you want to, I can put up a group page specific to this chip type, documenting the chip type (and either link or host those annotation files). Might be useful for a future fellow researcher. It's your call. /Henrik On Fri, Jan 30, 2009 at 12:08 PM, David Rosenberg <[email protected]> wrote: > > I am receiving the following errors when attempting to perform allelic > crosstalk calibration on a dataset using a custom CDF. I don't know > if this is indicative of errors in the internal structure of the CDF, > or if there are parameters that I must pass to > AllelicCrosstalkCalibration due to the properties of the CDF (i.e. # > of chromosomes, etc.) > > >> library("aroma.affymetrix") > Loading required package: R.utils > Loading required package: R.oo > Loading required package: R.methodsS3 > R.methodsS3 v1.0.3 (2008-07-02) successfully loaded. See ?R.methodsS3 > for help. > R.oo v1.4.6 (2008-08-11) successfully loaded. See ?R.oo for help. > R.utils v1.1.3 (2009-01-12) successfully loaded. See ?R.utils for > help. > Loading required package: aroma.core > Loading required package: R.cache > R.cache v0.1.7 (2008-02-27) successfully loaded. See ?R.cache for > help. > Loading required package: R.rsp > R.rsp v0.3.4 (2008-03-06) successfully loaded. See ?R.rsp for help. > Type browseRsp() to open the RSP main menu in your browser. > Loading required package: matrixStats > Loading required package: digest > Loading required package: aroma.light > aroma.light v1.11.1 (2009-01-12) successfully loaded. See ?aroma.light > for help. > aroma.core v1.0.0 (2009-01-12) successfully loaded. See ?aroma.core > for help. > Loading required package: affxparser > Loading required package: R.huge > R.huge v0.1.6 (2008-07-03) successfully loaded. See ?R.huge for help. > Loading required package: aroma.apd > aroma.apd v0.1.3 (2006-06-14) successfully loaded. See ?aroma.apd for > help. > aroma.affymetrix v1.0.0 (2009-01-12) successfully loaded. See ? > aroma.affymetrix for help. >> >> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE) >> >> # Don't display too many decimals. >> options(digits=4) >> chipType="MOUSEDIVm520650" >> cdf<-AffymetrixCdfFile$byChipType("MOUSEDIVm520650") >> print(cdf) > AffymetrixCdfFile: > Path: annotationData/chipTypes/MOUSEDIVm520650 > Filename: MOUSEDIVm520650.CDF > Filesize: 463.91MB > Chip type: MOUSEDIVm520650 > RAM: 0.00MB > File format: v4 (binary; XDA) > Dimension: 2572x2680 > Number of cells: 6892960 > Number of units: 973990 > Cells per unit: 7.08 > Number of QC units: 4 >> gi<-getGenomeInformation(cdf) >> print(gi) > UgpGenomeInformation: > Name: MOUSEDIVm520650 > Tags: DMR20090129 > Pathname: annotationData/chipTypes/MOUSEDIVm520650/ > MOUSEDIVm520650,DMR20090129.ugp > File size: 4.64MB > RAM: 0.00MB > Chip type: MOUSEDIVm520650 >> si<-getSnpInformation(cdf) >> print(si) > UflSnpInformation: > Name: MOUSEDIVm520650 > Tags: DMR20090129 > Pathname: annotationData/chipTypes/MOUSEDIVm520650/ > MOUSEDIVm520650,DMR20090129.ufl > File size: 3.72MB > RAM: 0.00MB > Chip type: MOUSEDIVm520650 > Number of enzymes: 2 >> acs<-AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE)) >> print(acs) > AromaCellSequenceFile: > Name: MOUSEDIVm520650 > Tags: DMR20090129 > Pathname: annotationData/chipTypes/MOUSEDIVm520650/ > MOUSEDIVm520650,DMR20090129.acs > File size: 170.91MB > RAM: 0.00MB > Number of data rows: 6892960 > File format: v1 > Dimensions: 6892960x26 > Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, > raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, > raw > Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, > 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 > Footer: <createdOn>20090129 12:45:11 CST</ > createdOn><platform>Affymetrix</platform><chipType>MOUSEDIVm520650</ > chipType> > Chip type: MOUSEDIVm520650 > Platform: Affymetrix >> csR<-AffymetrixCelSet$byName("mDIV/testset", cdf=cdf) >> print(csR) > AffymetrixCelSet: > Name: testset > Tags: > Path: rawData/mDIV/testset/MOUSEDIVm520650 > Platform: Affymetrix > Chip type: MOUSEDIVm520650 > Number of arrays: 44 > Names: SNP_mDIV_A10-10_081308, SNP_mDIV_A10-201_091708, ..., > SNP_mDIV_A9-9_081308 > Time period: 2008-08-13 15:39:47 -- 2008-09-18 00:20:33 > Total file size: 2899.65MB > RAM: 0.06MB > There were 50 or more warnings (use warnings() to see the first 50) >> acc<-AllelicCrosstalkCalibration(csR, model="CRMAv2") >> print(acc) > AllelicCrosstalkCalibration: > Data set: testset > Input tags: > User tags: * > Asterisk ('*') tags: ACC,ra,-XY > Output tags: ACC,ra,-XY > Number of files: 44 (2899.65MB) > Platform: Affymetrix > Chip type: MOUSEDIVm520650 > Algorithm parameters: (rescaleBy: chr "all", targetAvg: num 2200, > subsetToAvg: chr "-XY", mergeShifts: logi TRUE, B: int 1, flavor: chr > "sfit", algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075 > 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98) > Output path: probeData/testset,ACC,ra,-XY/MOUSEDIVm520650 > Is done: FALSE > RAM: 0.01MB >> csC<-process(acc, verbose=verbose) > 20090130 14:03:43|Calibrating data set for allelic cross talk... > Error in if (any(units < 1)) stop("Argument 'units' contains non- > positive indices.") : > missing value where TRUE/FALSE needed > 20090130 14:03:43|Calibrating data set for allelic cross talk...done >> traceback() > 13: readCdfCellIndices(pathname, ...) > 12: getCellIndicesChunk(getPathname(this), units = unitsChunk, ..., > verbose = verbose) > 11: fcn(idxs[ii], ...) > 10: lapplyInChunks.numeric(units, function(unitsChunk) { > cdfChunk <- getCellIndicesChunk(getPathname(this), units = > unitsChunk, > ..., verbose = verbose) > res <- vector("list", length(unitsChunk)) > res[[1]] <- unlist(cdfChunk, use.names = useNames) > res > }, chunkSize = 1e+05, useNames = useNames, verbose = verbose) > 9: lapplyInChunks(units, function(unitsChunk) { > cdfChunk <- getCellIndicesChunk(getPathname(this), units = > unitsChunk, > ..., verbose = verbose) > res <- vector("list", length(unitsChunk)) > res[[1]] <- unlist(cdfChunk, use.names = useNames) > res > }, chunkSize = 1e+05, useNames = useNames, verbose = verbose) > 8: getCellIndices.AffymetrixCdfFile(cdf, units = subset, useNames = > FALSE, > unlist = TRUE) > 7: getCellIndices(cdf, units = subset, useNames = FALSE, unlist = > TRUE) > 6: getSubsetToAvg.AllelicCrosstalkCalibration(this) > 5: getSubsetToAvg(this) > 4: getParameters.AllelicCrosstalkCalibration(this) > 3: getParameters(this) > 2: process.AllelicCrosstalkCalibration(acc, verbose = verbose) > 1: process(acc, verbose = verbose) > > > --~--~---------~--~----~------------~-------~--~----~ 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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