[BioC] vsn: L-BFGS-B needs finite values of fn (was: help in
huber at ebi.ac.uk
Tue Mar 22 22:15:19 CET 2005
> vsn normalisation
> vsn: 474 x 2 matrix (1 stratum).
> 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.
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
> pmt1rew at 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
>> which returns the following error message
>> begin of normalisation
>> the following hybridisation index(es) are used in normalisation step 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 :
>> vsn normalisation
>> vsn: 474 x 2 matrix (1 stratum). Please wait for 10 dots: ......Error:
>> 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 =
>> 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
>> Hope you can help. Thanks
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
Phone: +44 1223 494642
Fax: +44 1223 494486
More information about the Bioconductor