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arrayQualityMetrics
Correct the matching of slots between R code and man pages

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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
Change the sampleNames call for NChannelSet

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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
Added missing Suggests in CCl4.
Added missing import.
Removed unneeded geneplotter dependency.

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arrayQualityMetrics
Fixing vignette building
Corrected typo ALLML in DESCRIPTION

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arrayQualityMetrics
Call aqm.spatial for AffyBatch automatically

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arrayQualityMetrics
Fix colours boxplot when 2 col but no groups
fix typos in report

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arrayQualityMetrics
Fix usage of grouprep and better presentation of boxplot and densityplot using lattice. Should be faster as well to draw the boxplots now

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arrayQualityMetrics
Correct man and vignette for boxplot and density usage with grouprep
Grouprep for density

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arrayQualityMetrics
Use cairo instead of default for mac in write.report

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arrayQualityMetrics
Correction of man page for qcs

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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
legend of PCA more complete
Add datasets for examples

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arrayQualityMetrics
Fix the vignette

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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
added PCA

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arrayQualityMetrics
Add a PCA function

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arrayQualityMetrics
Details in formatting the report

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arrayQualityMetrics
Update aqm vignette and small changes in report formatting.

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arrayQualityMetrics
Update vignette aqm

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arrayQualityMetrics
Fix Namespace and BeadLevelList method

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arrayQualityMetrics
Better formatting

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arrayQualityMetrics
Corrected vignette dependencies and add descriptions in man pages that missed it.

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arrayQualityMetrics
New version of the package with more modularity. Each aqm function can
be called separately and produces an object containing the plot, the
legend, the title, the scores and the outliers. Then function aqm.plot
allows the plotting and the file writereport.r contains the code to
create the full report.
The vignette needs to be done.

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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
trying to sort out some of the name space issues

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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
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.

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arrayQualityMetrics
Adding a missing vignette dependency.

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arrayQualityMetrics
Modifications in XYfromGAL after Youssef Darzi comments
Updates to the vignette
update vignette

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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
Fix the rg2ncs function

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arrayQualityMetrics
Include a method for RGLists.
Modify addXYfromGAL to make it work on csv files and tabulated files.

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arrayQualityMetrics
correcting the parenthesis and add help on rg2ncs

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arrayQualityMetrics
add a function to convert RGList into an NChannelSet to prepare the data before using aQM

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arrayQualityMetrics
- same colour groups across plots

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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
Correcting the legend when using grouprep =TRUE

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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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