NEWS

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HTqPCR 1.9

SIGNIFICANT USER-VISIBLE CHANGES

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

NEW FEATURES

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

BUG FIXES

• o

HTqPCR 1.7

SIGNIFICANT USER-VISIBLE CHANGES

• o

NEW FEATURES

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

BUG FIXES

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

HTqPCR 1.5

SIGNIFICANT USER-VISIBLE CHANGES

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

NEW FEATURES

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

BUG FIXES

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

HTqPCR 1.3

SIGNIFICANT USER-VISIBLE CHANGES

• o

NEW FEATURES

• Added dupcor parameter to limmaCtData.

BUG FIXES

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

HTqPCR 1.1

SIGNIFICANT USER-VISIBLE CHANGES

• 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

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

BUG FIXES

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

HTqPCR 1.0

SIGNIFICANT USER-VISIBLE CHANGES

• First submission of HTqPCR to BioConductor.