Hi, have a look at thread 'MOUSEDIVm520650 and CRMAv2' started on Nov 5, 2010:
https://groups.google.com/d/topic/aroma-affymetrix/MEGCiXrPA80/discussion 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 to http://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/discussion /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 as > http://www.mail-archive.com/aroma-affymetrix@googlegroups.com/msg01458.html: > > 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 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. 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/
