Dear Rebecca, > vsn normalisation > vsn: 474 x 2 matrix (1 stratum). > Error: > L-BFGS-B needs finite values of fn This error can occur when the likelihood has a shallow maximum, and the numerical optimizer runs into nirvana. I have recently updated the vsn package (version 1.5.5) so that this convergence problem is now avoided in some cases, and if not it produces a more meaningful error message than the one you got. Following recommendations to increase the stability of the algorithm and get better convergence: - use a higher value of lts.quantile - apply it to your whole 474 x 6 matrix at once, rather than three times to individual 474 x 2 matrices. The non-convergence can occur e.g. if the two columns are (nearly) identical - then there isn't enough variability to estimate the noise parameters of the error model used in vsn. Cheers, Wolfgang Andreas Buness wrote: > Dear Rebecca, > > the error 'L-BFGS-B' is related to the normalisation method 'vsn' > and your specific data set. So e.g., if using 'loess' instead, the > error would not occur. Otherwise possibly change the options, e.g. > skip the argument 'hybridisationGroups' or specify 'pstart' for 'vsn' > in the function call of 'normalise'. cf. the discussion in > > https://stat.ethz.ch/pipermail/ bioconductor/2004-May/004738.html > https://stat.ethz.ch/pipermail/ bioconductor/2004-June/005076.html > > Non-unique identifiers cannot be used to label matrix rows without > ambiguity. But the call of 'qualityParameters' with argument > 'spotIdentifier="Name"' as specified in the vignette should > give you results regarding your replicate spots. > > Hope this helps, best regards > Andreas > > > > pmt1rew@leeds.ac.uk wrote: > >> Dear all >> >> I have a set of raw data values, 2 channels and 3 hybridisations. I have >> created an array of dimension 474x2x3 and am now trying to normalise >> the data, >> each hybridistaion separately. I have installed the arrayMagic >> package and >> used the command >> >> >> eSRG<-normalise(arrayDataobject,method="vsn",hybridisationGroups="s lideBySlide",spotIdentifier="Name") >> >> >> which returns the following error message >> >> begin of normalisation >> the following hybridisation index(es) are used in normalisation step 1 : >> 1 >> vsn normalisation >> vsn: 474 x 2 matrix (1 stratum). Please wait for 10 dots: .......... >> the following hybridisation index(es) are used in normalisation step 2 : >> 2 >> vsn normalisation >> vsn: 474 x 2 matrix (1 stratum). Please wait for 10 dots: ......Error: >> L-BFGS-B >> needs finite values of fn >> >> >> My data matrix contains no zeros or negative values or Inf and there >> are are no >> coloumns which contain all the same value. Hope that you can help >> with why and >> how to amend it? >> >> Furthermore, I have a column of 474 gene names. They are non- unique >> since I >> have six replicates per gene. Thus I have used used spotIdentifier = >> "Name" >> which is one of my column names. I get the line >> >> non-unique identifiers found in getSpotAttr(arrayDataObject) >> no spot/gene names have been added to the exprSetRG in normalise >> >> however when I call qPL anything to do with replicate spot returns a >> value of >> NA? >> >> Hope you can help. Thanks >> >> Rebecca >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber