help in arrayMagic?
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@pmt1rewleedsacuk-1154
Last seen 7.1 years ago
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="slid eBySlide",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
vsn vsn • 702 views
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@andreas-buness-821
Last seen 7.1 years ago
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="sl ideBySlide",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 -- -------------------------------------------------------------- Andreas Buness Molecular Genome Analysis (B050) German Cancer Research Center room TP3 2.109 Im Neuenheimer Feld 580 phone ++49 6221 42-4716 D-69120 Heidelberg Germany ----------- http://www.dkfz.de/abt0840/home/buness/WWW/ ------
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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
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