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Bioconductor Changlog.
Thu, 25 Jun 2009
lumi
initialize,LumiBatch accepts either exprs/se.exprs or assayData, to be
consistent with initialize,eSet requirements
additional housekeeping to bring docs / code in line
lumi
Some updates related with changes of ID mapping packages
lumi
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
lumi
Removed unneeded geneplotter dependency.
lumi
Minor updates related with annotation packages
lumi
Minor updates of lumiR and GEO submission functions
Minor updates of lumiR and GEO submission functions
lumi
fixed Rdversion 2 parser warnings
lumi
fixed some warnings message shown in Bioconductor checking results
Fixed some warning messages shown in the Bioc check results.
lumi
update related with GEO submission
Some updates related with submission of GEO files
lumi
removed quotes from do.call
lumi
Changes due to the removal the .db suffix of the Illumina ID Mapping package names (resolve the confliction with the convention of Bioconductor annotation packages), e.g., lumiHumanIDMapping.db as lumiHumanIDMapping
lumi
Update addNuID2lumi function to fix a bug due to the change of R 2.8
lumi
Fixed a small bug in bgAdjust function (background correction)
lumi
Fixed a small bug in bgAdjust function (background correction)
lumi
Add NameSpace to the library
lumi
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
lumi
Temporary removed the NAMESPACE
lumi
Temporary removed the NAMESPACE
lumi
Add NAMESPACE to the lumi package
added a missing dependency
lumi
Add description of GEO submission
Add description of GEO submission functions
lumi
lumiR can read BeadStudio file with different ProbeID colname
lumi
Updated replacement functions of detection and beadNum functions to allow removing them. For example:
detection(x.lumi) <- NULL
will remove the detectoin element in the assayData slot.
lumi
1. Add GEO submission functions
2. Some minor updates of ID mapping functions
lumi
Fixed a bug to handle the missing BeadNumber columns in the addNuID2lumi function
lumi
Updated some ID mapping related functions and vignettes
lumi
Removed usage (or reference) to pstricks tex style in BioC vignettes.
lumi
Update the diagrams in vignettes
lumi
Update the ID mapping functions and related documents.
lumi
Changed the function name of addNuId2lumi as addNuID2lumi (old function is still usable, but will be outdated.).
Changed the function addNuId2lumi name as addNuId2lumi
1. Added Illumina ID Mapping functions based on ID Mapping metadata packages.
2. Updated the vignettes and other related functions
lumi
update the citation information
lumi
Add verbose parameter to the functions
lumi
Add "QC" options in the lumiR and lumiR.batch and some related updates.
lumi
1. Updated the code of inputing control probe data.
2. lumiExpresso by default will do background adjustment if controlData available.
lumi
Allow doing inverseVST for all normalization methods following VST methods
lumi
Update getControlData function to allow inputting "control gene data.txt"
lumi
Add citations
lumi
Add smoothScatter option for the pairs and MAplot, and updated related help files and vignette.
Add random seed parameter for the subsetting related functions
lumi
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
lumi
Add a vignette about Illumina annotation
lumi
update lumi vignette