NEWS

lumi 2.5.1

release date: 04/23/2011

1. Adding supports for Infinium 450K methylation microarrays, which includes updating the color bias correction and other related functions.

lumi 2.3.8

release date: 01/31/2011

1. Bug fix related with Methylation File GEO submission

lumi 2.3.7

release date: 01/22/2011

1. Moved the MethyLumiM class and related methods from lumi to methylumi package 2. Add some methylation status estimation functions and updated vignette

lumi 2.3.5

release date: 01/12/2011

1. Add methylated.N and unmethylated.N matrix to the assayData slot of the MethyLumiM class

Thanks Tim Tiche, Jr. adding this

lumi 2.3.4

release date: 01/03/2011

1. Add controlData slot to the MethyLumiM class 2. Update functions handling controlData, which include: addControlData2methyLumiM, estimateMethylationBG, getControlType, plotControlData and lumiMethyR

lumi 2.3.3

release date: 12/29/2010

1. Add functions of estimating methylation status

lumi 2.3.2

release date: 12/21/2010

Multiple minor updates, which includes

1. vignettes of methylation analysis 2. annotation field of example.lumi dataset 3. detectionCall for methylation data 4. Auto check of parameter validation of lumiExpresso

lumi 2.3.1

release date: 11/08/2010

1. Multiple updates related with methylation analysis 2. Update of GEO submission file, make it be able to create GEO submission file based on a data matrix 3. Update of getChipInfo to make it be able to check based on address IDs

lumi 2.1.5-8

release data: 10/11/2010

1. Add a treatment and control example dataset 2. many updates of vignette 3. Add lumiMethyR function to wrap the methylumiR function from methylumi package 4. add the addColorChannelInfo function in case of no color channel information was included in the data.

lumi 2.1.4

release data: 09/22/2010

1. Enable lumiMethyB, lumiMethyC and lumiMethyN to run user defined functions 2. update of vignette

lumi 2.1.3

release data: 09/17/2010

1. Major update of the package by adding many functions related with Illumina Methylation microarray analysis. 2. Add the vignette of analyzing Illumina Infinium methylation microarray data

lumi 2.1.2

release data: 08/28/2010

1. Import several classes and functions from methylumi package for methylation analysis 2. Organize all generic functions together in a new file: AllGnereics.R

lumi 2.1.1

release data: 08/25/2010

1. Add na.rm setting to lumiB, lumiT and lumiN (Thanks Wieliang Qiu from Harvard reporting this!)

lumi 2.1.0

release data: 08/16/2010

1. Add Illumina Methylation data analysis components 2. Change the package dependence as NameSpaces

Sorry, many many updates and fixes not reported here

lumi 1.5.15-1.5.16

release data: 02/08/2008

1. The default normalization method is changed as 'quantile' instead of 'rsn'. 2. update lumiR for the changes of BeadStudio output.

lumi 1.5.10-1.5.14

release data: 02/03/2008

1. lumiR can also input the annotation information outputted by BeadStuio 2. Add plot functions dealing with the control probe data outputted by BeadStudio.

lumi 1.5.1-1.5.9

release data: 12/05/2007

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 1.3.27-1.3.37

release data: 09/30/2007

1. update the code to make vst accept negative values. 2. fixed bug of combine and subset functions dealing with controlData slot 3. add bg.Adjust background adjustment function to deal with the control probe information 4. add lumiR.batch function to input multiple files in batch 5. remove stdCorrection parameter from lumiR to lumiT, which converts the standard error of the mean to standard deviation in variance stabilization. 6. other small updates of help and vignette

Thanks Wei Shi and Gordon Smith for reporting problems and suggestions for improvements

lumi 1.3.18-1.3.26

release data: 08/25/2007

1. Updated the vst function in version 1.3.25. (estimate the c3 based on the background probes). 2. Updated the inverseVST and other related functions to allow the recover to the raw scale of the preprocessed data. 3. Added the evaluation of VST vignette 3. Updated the lumi vignette

lumi 1.3.16-1.3.17

release data: 07/11/2007

1. Add the correction of the STDEV column values of the BeadStudio output file (transfer the standard error of the mean as the standard deviation). 2. Updated the vignette.

Thanks Gordon Smith provided the information of STDEV column of BeadStudio output file

lumi 1.3.12-1.3.15

release data: 06/29/2007

1. Updated the vignette with added performance evaluation section. 2. Added "dec" option in lumiR function 3. Add density funciton 4. Allow user to select and customize the input columns of BeadStudio output files

Thanks Renee McElhaney for checking the vignette, Martin Morgan, Ingrid H. G. Østense and Michal Blazejczyk for the suggestion or reporting problems

lumi 1.3.11

release data: 06/16/2007

Add the annotation library information when run addNuId2lumi function

Thanks Vincent Carey (Harvard) for the suggestion

lumi 1.3.0-1.3.10

release date: 04/22/2007-06/15/2007

Major updates

1. All the major functions compatible with ExpressionSet class 2. presentCount was removed from the featureData. use detectionCall function to estimate presentCount 3. lumiR function now allows user to select the input data columns 4. Add lumiB function for background correction 5. lumiExpresso function to encapsulate all preprocessing functions 6. Vignette tutorial has major updates.

Thanks Ryan Gordon, DeokHoon Kim, Danilo Licastro, Matthias Kohl, Ezhou Lori Long (NIH), Sean Davis (NIH) and others for the suggestions and reporting problems

lumi 1.1.7

release date: 04/22/2007

1. Major updates of the vignette. 2. A simpleOutput option was added for the lumiT function. 3. Added nuID and targetID/probeID mapping functions.

lumi 1.1.4-6

release date: 04/17/2007

1. Updated lumiR function for better robustness. 2. Added subset parameter to all plot functions. 3. Add 'forcePositive' method to the lumiB function to avoid negative values. 4. Other related updates.

lumi 1.1.3

release date: 04/12/2007

1. Fixed the bug of combine function.

Thanks Jiexin Zhang (M.D. Anderson Cancer Center) finding the bug

lumi 1.1.2

release date: 04/11/2007

1. Updated lumiR to compatible with BeadStudio output file without header

lumi 1.1.0

release date: 03/24/2007

1. Updated lumiR to compatible with BeadStudio 3.0 output format 2. Removed LumiQC class and added QC slot in the LumiBatch class 3. Updated the functions related with updates 1 and 2

Thanks Sean Davis (NIH) and Michael Stevens (Washington University) for providing BeadStudio 3.0 files and testing

lumi 1.0.10

release date: 03/20/2007

1. Updated lumiN.rsn to allow the targetArray to be vector or LumiBatch object with one sample 2. Update the help documents

Thanks Jiexin Zhang (M.D. Anderson Cancer Center) providing the suggestion of targetArray

lumi 1.0.9

release date: 03/18/2007

1. Updated lumiN to make it accept ExpressionSet inherited object or data matrix 2. Update the some help files

lumi 1.0.7

release date: 02/20/2007

1. Updated the vignette and lumiN.rsn function

lumi 1.0.6

release date: 02/15/2007

1. Updated the combine method of LumiBatch class, addNuId2lumi, lumiR for better adaptiveness.

lumi 1.0.5

release date: 02/14/2007

1. Updated lumiR function to allow directly adding nuID when reading the data; 2. Updated addNuId2lumi to add the tracking history:

lumi 1.0.4

release date: 02/08/2007

1. Updated lumiR function to make it compatible with R 2.5; 2. Updated addNuId2lumi and lumiN function to fix some typos.

Thanks Jean-Eudes DAZARD (Case Western Reserve University) reporting this problem

lumi 1.0.3

release date: 01/21/2007

1. Updated lumiR and addNuId2lumi functions to allow them mapping TargetId or ProbeId to nuID;

lumi 1.0.2

release date: 01/01/2007

1. Changed the S3 function "plot.lumiQC" as the S4 function "plot" with signature "LumiQC, missing"; 2. Added S4 function "hist" with signature "ExpressionSet"; 3. Added rownames duplication checking code in the "addNuId2lumi" and "lumiR" functions; 4. Added varMetadata information in the LumiBatch object produced in "lumiR" function; 5. Updated the help and tutorial files.

Thanks Kevin Coombes (M.D. Anderson Cancer Center) for the testing and suggestions of the lumi package

lumi 1.0.1

release date: 12/11/2006

1. Updated the summary (show) functions of LumiBatch and LumiQC objects; 2. Added subsetting code for the LumiQC and LumiBatch objects; 3. Updated the help and tutorial files.