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=item Missing argument for command I<com>

Indicates that command line option I<com> requires an argument but none was supplied.

=item Input data file not supplied

Indicates that an input data file (final command line argument) was not supplied.

=item Command line option -t must be given when -p dual is used

Indicates that the -t command line option for supplying a test dataset is missing. This
must be given when -p dual is used.

=item Unable to open supplementary file I<filename>

Indicates that the file I<filename> given as argument to the C<-s> option was not readable.

=item Wrong number of columns in supplmentary file at line I<index>

Indicates that the number of columns at line I<index> differs from the number of
column names on the first row. The first row defines the correct number of columns, and
every subsequent row must have the same number of columns.

=item Missing sample name in supplmentary file at line I<index>

Indicates that the sample name (first column) is missing on line I<index>.

=item Class variable I<classVar> in supplementary file does not have two classes

Indicates that the class variable column with name I<classVar> contains fewer/more than
two different class labels. Since the algorithm has been designed to only handle binary
classification, a classification variable is only allowed to have two class labels.

=item Unable to open input/testset data file I<filename>

Indicates that the input/testset data file I<filename> was not readable. The input data
file must be given as the last command line argument. A testset data file must be
supplied using the -t option when the C<-p dual> option is used.

=item Unable to create new data file I<filename>

Indicates that the new input data file with meta data could not be written.

=item No samples in input/testset data file

Indicates that the input/testset data file, which is supposed to contain the expression data table,
does not contain any sample columns.

=item CLASSVAR class label equals NULL CLASS in input/testset data file

Indicates that one of the I<classLabel> values for a #CLASSVAR meta data row is equal
to the null class symbol #NA. The I<classLabel> values are the class labels for the
classification variable and cannot be equal to #NA, because this symbol is reserved as
a null class symbol.

=item Missing meta data for classification variable I<classVar> in input/testset data file

Indicates that the classification variable name given to the -c option is missing in
the meta data of the input or testset data file.

=item CLASSMEM vector for I<classVar> and sample vector have different lengths in input/testset data file

Indicates that the number of class labels on the #CLASSMEM row for I<classVar> is
different from the number of samples in the input or testset data file.

=item Invalid class label in I<classVar> CLASSMEM vector in input/testset data file

Indicates that one or more class labels on the #CLASSMEM row for I<classVar> are
invalid. Valid class labels are those given on the #CLASSVAR row for I<classVar> and
the null class symbol #NA.

=item Class I<classLabel> for classification variable I<classVar> has zero members in input/testset data file

Indicates that no samples have the class label I<classLabel> for classification
variable I<classVar>. This means that classification cannot be carried out, since all
samples belong to the same class.

=item Wrong number of columns in input/testset data file at probe I<index>

Indicates that a probe row in the input or testset data file has wrong number of columns with respect
to the number of samples.

=item Probe C<probename> in input data file not found in testset data file

Indicates that a probe in the input data file is missing in the testset. For classification
to be carried out using two datasets, all probes in the input data file must be present
in the testset.

=item Unable to create output file

Indicates that output files were not writable in the output folder.

=back

=head1 SEE ALSO

The publication describing the algorithm can be found in PubMed by this link:
L<http://www.ncbi.nlm.nih.gov/pubmed?Db=pubmed&Cmd=DetailsSearch&Term=23467331%5Buid%5D>

=head1 EXPORT

None by default. The runClassifier subroutine is exported on request.

=head1 AUTHOR

Benjamin Ulfenborg, E<lt>wolftower85@gmail.comE<gt>

=head1 COPYRIGHT AND LICENSE

Copyright (C) 2012 by Benjamin Ulfenborg

This module is free to use, modify and redistribute for academic purposes.

=cut