Hi, see below.
On Wed, Jan 19, 2011 at 6:34 PM, yupu <yupuli...@gmail.com> wrote: > Hi, > > I followed the advice to filter out some PCR fragment based on length > ( < 450 | > 2000). > > But i still run into the same error (see below). I am not sure what > went wrong....... > > Thanks, > Yupu > > > 20110119 00:18:09| Array #1 of 36 ('KP_17124_NT_MOUSEDIVm520650')... > V1 V2 > Min. : 450 Min. : 450 > 1st Qu.: 700 1st Qu.: 689 > Median : 958 Median : 945 > Mean : 1065 Mean : 1050 > 3rd Qu.: 1408 3rd Qu.: 1385 > Max. : 2000 Max. : 2000 > NA's :1225618 NA's :1224870 > int [1:2291870] 1 2 3 4 5 6 7 8 9 10 ... > UflSnpInformation: > Name: MOUSEDIVm520650 > Tags: na30,mm9,filter450-2000,HB20101105 > Full name: MOUSEDIVm520650,na30,mm9,filter450-2000,HB20101105 > Pathname: annotationData/chipTypes/MOUSEDIVm520650/ > MOUSEDIVm520650,na30,mm9,filter450-2000,HB20101105.ufl > File size: 9.38 MB (9835569 bytes) > RAM: 18.76 MB > Chip type: MOUSEDIVm520650 > Number of enzymes: 2 > 20110119 00:18:17| Setting up predefined target functions... > 20110119 00:18:17| Target type: zero > 20110119 00:18:17| Setting up predefined target functions...done > 20110119 00:18:17| Getting cell matrix map... > 'UnitGroupCellMatrixMap' int [1:2458673, 1] 25 26 27 28 29 30 31 > 32 33 34 ... > 20110119 00:18:20| Getting cell matrix map...done > 20110119 00:18:20| Getting theta estimates... > 20110119 00:18:21| Thetas: > num [1:2458673, 1] 0 0 0 0 0 0 0 0 0 0 ... > num [1:2458673, 1] 0 0 0 0 0 0 0 0 0 0 ... > V1 > Min. :0 > 1st Qu.:0 > Median :0 > Mean :0 > 3rd Qu.:0 > Max. :0 These are all zeros. You have most likely forgotten to run fit() on the probe-level modelling step (AvgCnPlm). > 20110119 00:18:21| Getting theta estimates...done > 20110119 00:18:21| Calculating total signals... > 20110119 00:18:22| Total thetas: > num [1:2458673] 0 0 0 0 0 0 0 0 0 0 ... This says that too. /Henrik > 20110119 00:18:22| Calculating total signals...done > 20110119 00:18:22| Normalizing log2 signals... > 20110119 00:18:22| Log2 signals: > num [1:2458673] -Inf -Inf -Inf -Inf -Inf ... > Error in list(`source("yupu.preprocess.Mm.R")` = <environment>, > `eval.with.vis(ei, envir)` = <environment>, : > > [2011-01-19 00:18:23] Exception: Cannot fit normalization function to > enzyme, because there are no (finite) data points that are unique to > this enzyme: 1 > at throw(Exception(...)) > > > On Jan 14, 8:39 am, Henrik Bengtsson <henrik.bengts...@aroma- > project.org> wrote: >> Hi, >> >> have a look at thread 'MOUSEDIVm520650 and CRMAv2' started on Nov 5, 2010: >> >> https://groups.google.com/d/topic/aroma-affymetrix/MEGCiXrPA80/discus... >> >> There we noted that this is because Affymetrix no longer filters the >> fragment lengths in its annotation files. This means that all SNPs >> have fragment lengths reported for both enzymes in our UFL annotation >> files. In order to fit the fragment-length model, there have to be >> SNPs for which only one of the two enzymes have a fragment length. >> >> The workaround found, as explained in that thread, is to create a UFL >> where one turn very short or very long fragment length values intoNAs. >> In my Nov 5 reply to the above threat, there is a code example >> showing how to drop lengths < 450 bp or > 2000 bp creating a new UFL >> file. >> >> Hans-Ulrich (bcc:ed), did you create such a UFL file? Did that solve >> the problem? Would you mind sharing that UFL file here - I can upload >> it tohttp://aroma-project.org/chipTypes/MOUSEDIVm520650/. That will >> save others from having to do the same. >> >> BTW, it would be more convenient to add filter options to >> FragmentLengthNormalization. For a discussion on implementing that, >> see thread 'GenomeWideSNP_6 hg19' started on Dec 10, 2010: >> >> https://groups.google.com/d/topic/aroma-affymetrix/FgETqjjYz1U/discus... >> >> /Henrik >> >> >> >> On Thu, Jan 13, 2011 at 10:50 PM, yupu <yupuli...@gmail.com> wrote: >> > Hi, I have been using aroma to analysis our SNP6.0 array for a while. >> > Now we got data on the Mouse diversity array (MouseDIV__m520650). >> >> > I ran into problem at the fragmentation length normalization step -- >> > same >> > ashttp://www.mail-archive.com/aroma-affymetrix@googlegroups.com/msg0145... >> >> > Error in list(`process(fln, verbose = verbose)` = <environment>, >> > `process.FragmentLengthNormalization(fln, verbose = verbose)` = >> > <environment>, : >> >> > [2011-01-13 14:31:10] Exception: Cannot fit normalization function to >> > enzyme, because there are no (finite) data points that are unique to >> > this enzyme: 1 >> > at throw(Exception(...)) >> > at throw.default("Cannot fit normalization function to enzyme, >> > because there a >> > at throw("Cannot fit normalization function to enzyme, because there >> > are no (f >> > at normalizeFragmentLength.default(y, fragmentLengths = fl, >> > targetFcns = targe >> > at normalizeFragmentLength(y, fragmentLengths = fl, targetFcns = >> > targetFcns, s >> > at process.FragmentLengthNormalization(fln, verbose = verbose) >> > at process(fln, verbose = verbose) >> > 20110113 14:31:10| Normalizing log2 signals...done >> > 20110113 14:31:10| Array #1 of 36 >> > ('KP_17124_NT_MOUSEDIVm520650')...done >> > 20110113 14:31:10|Normalizing set for PCR fragment-length >> > effects...done >> >> > I am just wondering if there is any update on this issue. >> >> > Thanks, >> > Yupu >> >> > -- >> > 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 websitehttp://www.aroma-project.org/. >> > To post to this group, send email to aroma-affymetrix@googlegroups.com >> > To unsubscribe and other options, go tohttp://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/ > -- 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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