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Bioconductor Changlog.
Tue, 13 Oct 2009
lumi
Fixed a bug to handle the missing BeadNumber columns in the addNuID2lumi function
lumi
Modify lumiT to allow the situaiton without the se.exprs slot is missing for log2 and cubicRoot transformation.
lumi
1. Updated the code of inputing control probe data.
2. lumiExpresso by default will do background adjustment if controlData available.
lumi
Minor updates related with annotation packages
lumi
Add description of GEO submission
Add description of GEO submission functions
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
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
lumi
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
lumi
update lumi vignette
lumi
Minor updates of lumiR and GEO submission functions
Minor updates of lumiR and GEO submission functions
lumi
Some updates related with changes of ID mapping packages
lumi
Fixed a small bug in bgAdjust function (background correction)
lumi
Add "QC" options in the lumiR and lumiR.batch and some related updates.
lumi
version 1.5.1-1.5.9
1. Add functions dealing with the control probe data outputted by BeadStudio.
2. Extended VST algorithm for processing the Affymetrix data.
3. Add SSN (simple scaling normalization) algorithm for conservative normalization.
4. other updates of help and vignette
lumi
Add citations
lumi
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
lumi
fixed some warnings message shown in Bioconductor checking results
Fixed some warning messages shown in the Bioc check results.
lumi
Add NameSpace to the library
lumi
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
lumi
Add NAMESPACE to the lumi package
added a missing dependency
lumi
Update the ID mapping functions and related documents.
lumi
Add verbose parameter to the functions
lumi
1. Minor updates of lumiR, lumiR.batch, lumiN functions and documents.
2. Add ssn (Simple Scaling Normalization) function
lumi
Changed the default normalization algorithm of lumiN as quantile normalization.
updated lumiR to support the recent changes of BeadStudio output (about ProbeID)
lumi
1. Minor updates of lumiR, lumiR.batch, lumiN functions and documents.
2. Add ssn (Simple Scaling Normalization) function
lumi
Temporary removed the NAMESPACE
lumi
Add a vignette about Illumina annotation
lumi
fixed Rdversion 2 parser warnings
lumi
Removed commented out code that references newly defunct class phenoData.
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
Updated eSet definition and serialized object and bumped version number.
lumi
Temporary removed the NAMESPACE
lumi
Updated some ID mapping related functions and vignettes
lumi
Update the description field of some functions
lumi
update related with GEO submission
Some updates related with submission of GEO files
lumi
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
lumi
Fixed a small bug in bgAdjust function (background correction)
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
Removed unneeded geneplotter dependency.