It works. Thanks a lot. Jianming On Friday, January 4, 2013 2:43:04 PM UTC-5, Pierre Neuvial wrote:
> 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 <jianmi...@gmail.com<javascript:>> > 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-af...@googlegroups.com<javascript:> > > 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. 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/
