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Bioconductor Changlog.
Thu, 08 Nov 2007
annaffy
Minor fix to aaf.handler() so probe IDs will be annotated using the new .db packages.
altcdfenvs
Moved CITATION to inst/ so it is properly installed.
bumped version number
cellHTS2
Many updates related with making the preprocessing work-flow clearer and documenting the plate normalization methods. Details are given below:
- Adjust variance in normalizePlates function was set by default to "none".
- Regarding multi-channel data, both plate normalization steps (before and/or after channel summarization) are now allowed to be optional (in the last version, only the second one was optional).
- The steps of replicates scoring and summarization are now done by calling separate functions (scoreReplicates and summarizeReplicates) in order to make these two preprocessing steps more clearer.
- Added another scoring function (besides z-score) in "scoreReplicates" called NPI which applies NPI in a per-experiment fashion.
- Added "median" as a possible summarization method in "summarizeReplicates".
- Added an Appendix about the plate normalization methods available in cellHTS2 package to its main vignette.
- Added a description of the data preprocessing work-flow for 2-channel data in the corresponding vignette.
Rintact
I have changed my e-mail so that it matches with the bioc-devel list server
MCRestimate
debug vignette
xcms
Fixed a serious fillPeaks() bug introduced in version 1.9.5, which caused it to
silently fill in zero intensities for almost every missing peak
Added check in findPeaks.matchedFilter() for not picking filter artefacts
Changed default mzdiff parameter in findPeaks.centWave() from -0.02 to -0.001
biomaRt
Removed deprecated function getFeature as getBM is a more general function to do these types of queries. Added some extra argument checking for useMart, filterOptions and filterType functions.
graph
fixed updateGraph, it can now also update object from before graphData times