This file provides a brief description about the changes.


Changes summary:

Version 1.6.0
-------------

- Changed the name of the function "mt.rawp2adjp" to
  "mt.rawp2adjp.LPE" in order to avoid conflict with the original
  function from multtest library.

- Added the references to paired LPE - "LPEP library" and LPE for
  multiple conditions - "HEM library".

- Added an option "Bonferroni" in fdr.adjust.R to get Bonferroni
  adjusted p-values. (Though it is recommended to use FDR,
  Bonferroni adjusted method has been added here for users who want
  it.)

- Updated the document 'LPE.pdf' (hands on demonstration of LPE) in
  inst/doc.

Changes summary:

Version 1.3.0
-------------

Updated the file am.trans.R for faster computations.

Version 1.2.0
______________

- Created a project called "r-lpe" on sourceforge to get the most 
	recent files. One can keep track of changes and checkout 
	the latest version by anonymously checking out lpe from sf.net:
cvs -z3 -d:pserver:anonymous@cvs.sourceforge.net:/cvsroot/r-lpe co -P LPE

- Bug fix in baseOlig.error.step1 and baseOlig.error.step2:
	For some data sets, adjacent quantile values were same due
	to thresholding/nature of the data - which caused the number
	of genes to be selected for var(M) caluclation as 0, and
	hence there was an error: "Error in var(x) : 'x' is empty".

- Added a check in baseOlig.error.step1 and baseOlig.error.step2 to 
	see if min. value of variance does NOT go negative.

- Updated the email address. New address is: <nitin.jain@pfizer.com>

- Changed the default value of the parameter probe.set.name to NULL,
  so that if the GeneIDs are not provided, then rownames (1,2,3,...)
  are considered as GeneIDs.

- Changed the default argument of preprocess function 'lowess=TRUE' to FALSE.
  User should specify if they need lowess transformation.

- Added a reference (new published paper on "rank-invariant
  resampling for FDR calculations.


Version 1.1.5
______________



- More robust detection of outliers in two sample comparison.
  (Thanks to HyungJun Cho for the correction).

- Function lpe.R is broken in several small functions, easier to understand.

- Built under R 2.0.0