Hi, This thread should help you solving your problem:
https://groups.google.com/forum/?fromgroups=#!topic/aroma-affymetrix/S_wLLGcU8S0 Cheers, Pierre On Fri, Jan 4, 2013 at 6:58 PM, Foxchase <jianming....@gmail.com> wrote: > Dear Henrik, > I'm trying aroma.affymetrix for Affy's Affymetrix Mouse Diversity Genotyping > Array. I made the arom annotation files using Affy's na32's NetAffx files. > I use a public data 'GSE27691". Attached is the R history file. > When I followed the Vignette:CRMAv2 I got error at the step:> cesN <- > process(fln, verbose=verbose): > >> cesN <- process(fln, verbose=verbose) > 20130104 12:05:43|Normalizing set for PCR fragment-length effects... > 20130104 12:05:44| Identifying SNP and CN units... > types > 1 2 5 > 24 626135 1832538 > 20130104 12:05:44| subsetToUpdate: > int [1:2458673] 25 26 27 28 29 30 31 32 33 34 ... > 20130104 12:05:44| Identifying SNP and CN units...done > 20130104 12:05:44| Retrieving SNP information annotations... > UflSnpInformation: > Name: MOUSEDIVm520650 > Tags: > Full name: MOUSEDIVm520650 > Pathname: annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650.ufl > File size: 9.38 MB (9834930 bytes) > RAM: 18.76 MB > Chip type: MOUSEDIVm520650 > Number of enzymes: 2 > 20130104 12:05:44| Retrieving SNP information annotations...done > 20130104 12:05:44| Identifying the subset used to fit normalization > function(s)... > int [1:2292403] 25 26 27 28 29 30 31 32 33 34 ... > 20130104 12:05:44| Identifying the subset used to fit normalization > function(s)...done > 20130104 12:05:44| Shift: 0 > 20130104 12:05:44| onMissing: median > 20130104 12:05:44| Array #1 of 7 ('GSM685813')... > 20130104 12:05:44| Reading and filtering fragment lengths... > 20130104 12:05:44| Reading fragment lengths... > UflSnpInformation: > Name: MOUSEDIVm520650 > Tags: > Full name: MOUSEDIVm520650 > Pathname: annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650.ufl > File size: 9.38 MB (9834930 bytes) > RAM: 18.76 MB > Chip type: MOUSEDIVm520650 > Number of enzymes: 2 > 20130104 12:05:46| Summary of non-filtered fragment lengths: > int [1:2458673, 1:2] 2744 2744 2744 2744 2744 2744 572 572 572 572 ... > V1 V2 > Min. : 7 Min. : 7 > 1st Qu.: 616 1st Qu.: 542 > Median : 1149 Median : 999 > Mean : 1623 Mean : 1478 > 3rd Qu.: 2198 3rd Qu.: 2002 > Max. :32767 Max. :32767 > NA's :233634 NA's :233634 > 20130104 12:05:46| Reading fragment lengths...done > 20130104 12:05:46| Filtering fragment lengths... > 20130104 12:05:46| Filtering fragment lengths...done > 20130104 12:05:46| Reading and filtering fragment lengths...done > V1 V2 > Min. : 7 Min. : 7 > 1st Qu.: 616 1st Qu.: 542 > Median : 1149 Median : 999 > Mean : 1623 Mean : 1478 > 3rd Qu.: 2198 3rd Qu.: 2002 > Max. :32767 Max. :32767 > NA's :233634 NA's :233634 > int [1:2292403] 1 2 3 4 5 6 7 8 9 10 ... > UflSnpInformation: > Name: MOUSEDIVm520650 > Tags: > Full name: MOUSEDIVm520650 > Pathname: annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650.ufl > File size: 9.38 MB (9834930 bytes) > RAM: 18.76 MB > Chip type: MOUSEDIVm520650 > Number of enzymes: 2 > 20130104 12:05:47| Setting up predefined target functions... > 20130104 12:05:47| Target type: zero > 20130104 12:05:47| Setting up predefined target functions...done > 20130104 12:05:47| Getting cell matrix map... > 'UnitGroupCellMatrixMap' int [1:2458673, 1] 25 26 27 28 29 30 31 32 33 > 34 ... > 20130104 12:05:48| Getting cell matrix map...done > 20130104 12:05:48| Getting theta estimates... > 20130104 12:05:49| Thetas: > num [1:2458673, 1] 1047 477 3533 3499 3353 ... > num [1:2458673, 1] 1047 477 3533 3499 3353 ... > V1 > Min. : -143 > 1st Qu.: 1785 > Median : 4562 > Mean : 6687 > 3rd Qu.: 9142 > Max. :199787 > 20130104 12:05:49| Getting theta estimates...done > 20130104 12:05:49| Calculating total signals... > 20130104 12:05:49| Total thetas: > num [1:2458673] 1047 477 3533 3499 3353 ... > 20130104 12:05:49| Calculating total signals...done > 20130104 12:05:49| Normalizing log2 signals... > 20130104 12:05:49| Log2 signals: > num [1:2458673] 10 8.9 11.8 11.8 11.7 ... > [2013-01-04 12:05:50] Exception: Cannot fit normalization function, because > none of the units are on fragments from a single enzyme, or equivalently, > there exist no rows in argument 'fragmentLenghts' that only have one finite > value. > at #04. normalizeFragmentLength.default(y, fragmentLengths = fl, > targetFcns = targetFcns, > subsetToFit = subset, onMissing = onMissing, ...) > - normalizeFragmentLength.default() is in environment > 'aroma.light' > at #03. normalizeFragmentLength(y, fragmentLengths = fl, targetFcns = > targetFcns, > subsetToFit = subset, onMissing = onMissing, ...) > - normalizeFragmentLength() is in environment 'aroma.light' > at #02. process.FragmentLengthNormalization(fln, verbose = verbose) > - process.FragmentLengthNormalization() is in environment > 'aroma.affymetrix' > at #01. process(fln, verbose = verbose) > - process() is in environment 'aroma.core' > Error: Cannot fit normalization function, because none of the units are on > fragments from a single enzyme, or equivalently, there exist no rows in > argument 'fragmentLenghts' that only have one finite value. > In addition: Warning message: > NaNs produced > 20130104 12:05:50| Normalizing log2 signals...done > 20130104 12:05:50| Array #1 of 7 ('GSM685813')...done > 20130104 12:05:50|Normalizing set for PCR fragment-length effects...done >> print(cesN) > Error in print(cesN) : object 'cesN' not found >> > Please help me to figure out this issue. > Thank you > > Jianming > > -- > 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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