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.