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.
