CHANGES IN VERSION 1.9:

SIGNIFICANT USER-VISIBLE CHANGES

    o Altered plotCtCor to plot 1-correlation instead of correlation.
    o Altered qPCRset object to inherit from eSet. This extends the range
    of (meta) data that can be included.

NEW FEATURES

    o qPCRset now contains slots for phenoData, featureData, protocol
    experiment etc. inherited from eSet.
    o readCtData has been expanded to include file formats from multiple
    qPCR detection systems and vendors.

BUG FIXES

    o 

CHANGES IN VERSION 1.7:

SIGNIFICANT USER-VISIBLE CHANGES

    o 

NEW FEATURES

    o Added "geometric.mean" as a normalisation method.

BUG FIXES

    o Check for all-NA features in normalizeCtData rank-invariant methods.
    o Modified plotCtCategory to handle cases with only 1 sample.
    o Modified plotCtCategory to make colours more consistent.
    o Fix in deltaCt for normalization with NAs
    o Added warning in readCtData if there are NAs in input


CHANGES IN VERSION 1.5:

SIGNIFICANT USER-VISIBLE CHANGES

    o Made small adjustments to readCtData to make it more suitable for data
    from the Fluidigm platform.

NEW FEATURES

    o Added function plotCtVariation for displaying variation across 
    replicated features or samples.
    o Added function plotCtArray for visualising data from non-well plates
    (e.g. the Fluidigm platform)

BUG FIXES

    o Fixed bug in readCtData causing repeats of featureType and featurePos
    when n.data>1.
    o Corrected bugs for subsetting when flag() or featureCategory() are 
    missing.
    o Modified "history" slot for manually created qPCRset objects.

CHANGES IN VERSION 1.3:

SIGNIFICANT USER-VISIBLE CHANGES

    o 

NEW FEATURES

    o Added dupcor parameter to limmaCtData.

BUG FIXES

    o Fixed bug in plotCtOverview affecting sample names starting with "M".
    o Corrected rbind so all data frames contain characters, not factors.
    o Changed a "stop" to a "warning" in readCtData.
    o Corrected qPCRset subsetting when columns are selected multiple times.

CHANGES IN VERSION 1.1:

SIGNIFICANT USER-VISIBLE CHANGES

    o Add "history" slot to qPCRset object, instead of "normalized". 
    This means all operations (filtering, normalization etc.) performed 
    on the object can be retrieved with getCtHistory.

NEW FEATURES

    o n.data parameter to readCtData in case there are results from 
    multiple cards in each file.
     o getCt and setCt added as accessor and replacement functions (alias 
    for exprs).
    o Add "fold change" to the output from limmaCtData and ttestCtData.
    o Add p-value adjustment to ttestCtData.
    o Expanded functionality of plotCtPCA.
    o Added function changeCtLayout for data containing multiple samples 
    per 384 well plate.
    o Added rbind and cbind functions for combining qPCRset objects.
    o Added mannwhitneyCtData for Mann-Whitney test between samples.

BUG FIXES

    o Fixed a bug in readCtData regarding file paths.
    o Added "fake" featureNames to readCtData if not present in input.
    o Gives error if no column for Ct values is specified.
    o Fix bug in ttestCtData(.., paired=TRUE) (cf Jeremy Hetzel).
    o Added sample names to flag and featureCategory in readCtData.
    o Fixed bugs in plotting functions when exprs() only has 1 column.
    o Reset "par" after using plotCtCard.
    o Fixed bug with parameter "samples" in readCtData.
    o featureCategory only required if unR=TRUE and/or unD=TRUE in 
    plotCtCard.
    o In plotCtDensity, remove samples were all values=NA.
    o The internal function panel.Ct.cor adjusted to handle NAs.
    o Remove all samples with just NA in plotCtPCA.
    o Fixed bug in ttestCtData (results always reported as "OK" not
    "Undetermined")
    o Add sampleNames to flag() and featureCategory()

CHANGES IN VERSION 1.0:

SIGNIFICANT USER-VISIBLE CHANGES

    o First submission of HTqPCR to BioConductor.
