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Bioconductor Changlog.
Tue, 13 Oct 2009
arrayQualityMetrics
Add a PCA function
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arrayQualityMetrics
Corrected vignette dependencies and add descriptions in man pages that missed it.
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arrayQualityMetrics
Handling of ExonArrays
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arrayQualityMetrics
temporary fix to include scanDates to CCl4 so that the example of aqm.prepdata works fine
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arrayQualityMetrics
Optionnal spatial plots for faster reports in case of large arrays
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arrayQualityMetrics
Update aqm vignette and small changes in report formatting.
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arrayQualityMetrics
legend of PCA more complete
Add datasets for examples
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arrayQualityMetrics
- Update report legends of heatmap and spatial distribution
- Added a inst/script for the vignette so that Rnw is not run during check and build (too long).
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arrayQualityMetrics
Fix PCA colouring bug found by Matthew Huska.
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arrayQualityMetrics
Use cairo instead of default for mac in write.report
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arrayQualityMetrics
Better way of dealing with the factor of interest to show on the
heatmap, not "Covariate" anymore but one more argument: "intgroup"
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arrayQualityMetrics
patch given by Andrea Bisognin to avoid opening the nuse plot while running
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arrayQualityMetrics
Fixed a build issue on Mac by setting the bitmapType option to "cairo".
- Use of as() from the convert package instead of rg2ncs which has now been removed to avoid redundancy.
- Methods for MAList, marrayRaw and marrayNorm
Use lattice to draw the legend of the heatmap thanks to Deepayan's help.
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arrayQualityMetrics
Details in formatting the report
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arrayQualityMetrics
Corrected aqm.writereport.Rd
Add the help pages of the objects used in the man pages
Update the legend and the vignette
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arrayQualityMetrics
- same colour groups across plots
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arrayQualityMetrics
Fixing vignette building
Corrected typo ALLML in DESCRIPTION
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arrayQualityMetrics
Modifications in XYfromGAL after Youssef Darzi comments
Updates to the vignette
update vignette
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arrayQualityMetrics
version bump
fixed a typo
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arrayQualityMetrics
added PCA
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arrayQualityMetrics
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
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arrayQualityMetrics
add possibility of multiple sidebars on dendrogram, need to have better handling of position of legend on this plot
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arrayQualityMetrics
Added missing Suggests in CCl4.
Added missing import.
Removed unneeded geneplotter dependency.
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arrayQualityMetrics
Fix setwd of NChannelSet
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arrayQualityMetrics
Correcting the legend when using grouprep =TRUE
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arrayQualityMetrics
Update with the new version of beadarray
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arrayQualityMetrics
Rnw corrected
New version including scores
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arrayQualityMetrics
Fix Namespace and BeadLevelList method
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arrayQualityMetrics
- add argument grouprep for group representation. It allows to show the
boxplots and densityplots with colours according to their biological
group defined in intgroup.
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arrayQualityMetrics
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
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arrayQualityMetrics
Fix some buglets around na.rm and on.exit
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arrayQualityMetrics
- Fixing MA plots ordering
- Replacing setwd(olddir) by on.exit
- Create a logtransform function to handle the 0 values
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arrayQualityMetrics
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
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arrayQualityMetrics
Correction of man page for qcs
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arrayQualityMetrics
?\195?\130replaced if by switch when possible
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arrayQualityMetrics
minor tweak to add a hasGCinfo function
Added "results=hide" to two code chunks.
Since we now use a NAMESPACE, I checked that the vignette (in inst/scripts) runs without errors
or warnings and produces apparently the same result as before.
I removed the use of undefined variables sec3text, gctext, legendgc, legendgo, gotext from the call to
'report' in the arrayQualityMetrics method for beadLevelList.
I fixed typos and grammar in the report text.
Some Code Fixing.
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arrayQualityMetrics
Removed the data and modified the man pages to call only once the objects and have a reasonnable check time
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arrayQualityMetrics
Change score table and experiments/arrays
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arrayQualityMetrics
Fix the vignette
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arrayQualityMetrics
- Modify the boxplot.stats function so that it only detect as outlier the value larger than the others
- Move the on.exit at the right place of the code for AffyBatch
- Correct the logtransform function
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