unclear on error in affxparser
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Entering edit mode
@elizabeth-purdom-2486
Last seen 8 months ago
USA/ Berkeley/UC Berkeley
Hi, This is a question regarding a function in the affxparser package. I am trying to create a cdf using writeCdf and the inputted objects are lists I created myself (paring down an existing cdf). I get the following error "Number of elements in argument 'qcUnitLengths' does not match 'nUnits'" (traceback is below). I don't understand why the number of elements of 'qcUnitLengths' SHOULD match 'nUnits'. Aren't those entirely different lists with entirely different number of elements? It seems like it should match nQcUnits. Or is there actually a different error check going on that I'm failing and the outputted error message is wrong? I think something's probably off, since I know people who have used similar types of lists to create cdfs and presumably have not gotten this error. So I'll try to track it down assuming something doesn't match that should, but it would be helpful to know where to start... Thanks, Elizabeth Purdom I have the following traceback from the error I get running on a small test case of my code: > traceback() 5: stop("Number of elements in argument 'qcUnitLengths' does not match 'nUnits'") 4: .initializeCdf(con = con, nRows = cdfHeader$nrows, nCols = cdfHeader$ncols, nUnits = cdfHeader$nunits, nQcUnits = cdfHeader$nqcunits, refSeq = cdfHeader$refseq, unitnames = unitNames, qcUnitLengths = qcUnitLengths, unitLengths = unitLengths) 3: writeCdfHeader(con = con, cdfheader, unitNames = names(cdf), qcUnitLengths = qcUnitLengths, unitLengths = unitLengths, verbose = verbose) 2: writeCdf(outfile, cdfheader = hdr, cdf = outList, cdfqc = qc, overwrite = TRUE, verbose = 10) 1: createTranscriptCDF(cdfProbeset, csvAnnotFile, linesPerRead = 10, type = "extended", dirLoc = getwd()) cdf affxparser cdf affxparser • 450 views ADD COMMENT 0 Entering edit mode @kasper-daniel-hansen-2979 Last seen 13 months ago United States Hi Elizabeth This is clearly a typo in the error message. Your problem is that length(unitlengths) does not match nUnits. Does that help? (Next time you can track this down by downloading the source package and grep for the error message) Kasper On Nov 13, 2007, at 8:49 PM, Elizabeth Purdom wrote: > Hi, > This is a question regarding a function in the affxparser package. > I am > trying to create a cdf using writeCdf and the inputted objects are > lists > I created myself (paring down an existing cdf). I get the following > error "Number of elements in argument 'qcUnitLengths' does not match > 'nUnits'" (traceback is below). I don't understand why the number of > elements of 'qcUnitLengths' SHOULD match 'nUnits'. Aren't those > entirely different lists with entirely different number of > elements? It > seems like it should match nQcUnits. Or is there actually a different > error check going on that I'm failing and the outputted error > message is > wrong? I think something's probably off, since I know people who have > used similar types of lists to create cdfs and presumably have not > gotten this error. So I'll try to track it down assuming something > doesn't match that should, but it would be helpful to know where to > start... > Thanks, > Elizabeth Purdom > > I have the following traceback from the error I get running on a small > test case of my code: >> traceback() > 5: stop("Number of elements in argument 'qcUnitLengths' does not match > 'nUnits'") > 4: .initializeCdf(con = con, nRows = cdfHeader$nrows, nCols = > cdfHeader$ncols, > nUnits = cdfHeader$nunits, nQcUnits = cdfHeader$nqcunits, > refSeq = cdfHeader$refseq, unitnames = unitNames, > qcUnitLengths > = qcUnitLengths, > unitLengths = unitLengths) > 3: writeCdfHeader(con = con, cdfheader, unitNames = names(cdf), > qcUnitLengths = qcUnitLengths, unitLengths = unitLengths, > verbose = verbose) > 2: writeCdf(outfile, cdfheader = hdr, cdf = outList, cdfqc = qc, > overwrite = TRUE, verbose = 10) > 1: createTranscriptCDF(cdfProbeset, csvAnnotFile, linesPerRead = 10, > type = "extended", dirLoc = getwd()) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor