Library maanova
================

Version 1.13.2 & 1.13.3, Feb 9, 2009
- fixed issue where random terms were not getting passed to matest
  permutations when shuffle.method was set to "resid"
- fixed bad call to "Warning(...)" (should have been "warning(...)")
- fixed misc other minor documentation and metadata issues

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Version 1.13.1, Dec 5, 2008
- did minor documentation updates
- changed get(getOption("device"))() to dev.new() since getOption breaks in R 2.8
- removed bad reference to ttest.method in clustering code
- fixed error in summarytable.R where replicates would cause a failure

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Version 1.5.1, Aug 18, 2007

Modify the function 
Reconstruct the flow

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Version 1.4.1, Apr 17, 2007
1. added the function ma.svd() to call LAPACK function DGESVD directly. It 
works the same way as the old La.svd() in R-2.3.1 and earlier.

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Version 1.2.2, Mar 9, 2007

A rollback version to run on R-2.3.1 and earlier to avoid the the error
message La.svd() throw out.

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Version 1.4.0, Oct 3, 2006

version run on R-2.4.0. bump up version number according bioconductor's rule.

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Version 1.2.1, May 9, 2006
1. Changed the La.svd(X, method="dgesdd") to La.svd(X) since
La.svd(X, method="dgesdd" or "dgesvd") is deprecated. La.svd(X)'s 
default method is "dgesdd" from R-2.3.0.
2. Add comments in matest.Rd about test covariate in "contrast" and
"test type" section.

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Version 1.2.0, Apr 23, 2006
1. Hyuna Yang made these changes:
Instead of pooled p-value, p-value based on subset method 
is implemented in matest.R. Include option critical. 
2. Correct several places in the manual files from "transform" 
to "transform.madata"
3. Changed the La.svd(X,method="dgesvd") to La.svd(X,method="dgesdd")
in util.R since the La.svd(X, method="dgesvd" is deprecated from 
R-2.3.0.
4. Version number jumps from 0.98.8 to 1.2.0 in order to 
keep up with bioconductor version number
5. For R-2.3.0, In transform.madata.R file: 
Changed	transform.rawdata <- function(x, ...) 
     to	transform.rawdata <- function(`_data`, ...)
Changed transform.madata <- function(x,
	method=c("shift","glowess","rlowess","linlog","linlogshift"),
	lolim, uplim,
	f=0.1, iter=3, degree=1,
	cg=0.3, cr=0.3, n.bin=10,
	draw=c("screen", "dev", "off"), ...) to
     to transform.madata <- function(`_data`,
	method=c("shift","glowess","rlowess","linlog","linlogshift"),
	lolim, uplim,
	f=0.1, iter=3, degree=1,
	cg=0.3, cr=0.3, n.bin=10,
        draw=c("screen", "dev", "off"), ...)
  and the corresponding transform.madata.Rd file.           

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Version 0.98-7, Mar 4, 2005
I lost track of some changes. But:
1. Added function fill.missing to do missing data imputation
using KNN;
2. Added function exprSet2Rawdata to convert an object of
exprSet from BioConductor to an object or rawdata
3. Fix a small bug (dot color) in volcano
4. Other misc changes for submitting R/maanova to BioConductor
5. Wrote a Swave style vignette 

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Version 0.98-4, Mar 4, 2005
Add a new option test.type in matest function.
Then user can specify a contrast matrix for F test

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Version 0.98-3, Jan 6, 2005
Correct a bug in shuffle.maanova

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Version 0.98-2, Dec 10, 2004

Made lots of misc changes on R and Rd files to pass 
"R CMD check". Read to submit to CRAN.

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Version 0.98-1, Dec 6, 2004

Minor changes are:
1. Modify data shuffling method in matestutil.R.
Array and Dye structure need to be kept.

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Version 0.97-7 Sep 16, 2004
Minor changes are:
1. Modify several plot functions for new R version (1.9.1)
under Mac OSX. Basically the earlier R use macintosh()
function to plot but the newer version use quartz().

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Version 0.97-5 Aug 31, 2004
Minor changes are:
1. Modify matest.R to remove the possible correlation
problem in random number generation for clusters.

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Version 0.97-5 Aug 13, 2004

Minor changes are:
1. Add function Rmaanova.version
2. Modify matest.R and matestutil.R to reduce the memory usage

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Version 0.97-4 May 17, 2004

Minor changes are:
1. allow having no bootstrap (n.perm=1) in macluster function
Then consensus will draw cluster plots on observed data
2. Modify the calculation of x-axis value in volcano plot 

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Version 0.97-2 June 20, 2004

Major changes are:
1. Rewrite mixed using method of scoring;


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Version 0.97-1 May 17, 2004

Major changes are:

1. Remove adjdata field in "madata" object 
2. Replace "ftest" functino by new function "matest", which
is a combination of "ftest" and "test.Contrast". Modify data
shuffling method. 
3. Rename "smooth" "transform.madata".
4. Modify (simplify) the syntax for several functions, e.g., 
macluster, consensus, etc.
5. Add new option log.trans in "createData" to log transform
the raw data or not.
5. Misc changes for other functions, e.g., subset.madata, 
read.madata, write.madata, etc...



--------------------------
Version 0.96-1 
Change the package to work for N-dye system. The major changes include:

1. Input files:

o Data file
  - There's no change for data file format.
o Design file
  - User must have "Array" and "Dye" columns in the design file. 
  - User must have a "Sample" column in the design file. This is equivelent
    to "SampleID" in the older version.
  - User must not have columns called "Spot" or "Label" in design file.
  - All fields are treated as factors. They don't need to be
    continous integers.

2. Functions:

o read.madata:
  - ArrayName field is removed from rawdata and madata objects

o riplot and arrayview work only for 2-dye system.

o makeModel:
   - covairate can be fixed or random
   - terms in formula must be in the design file, except "Spot"
     for spot effect and "Label" for labelling effect.

o fitmaanova:
  - levels are made for all terms




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Version 0.95-3 11/21/2003
Minor changes:
o fix a bug in ftest.mixed.engine

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Version 0.95-2 11/21/2003

I lost track of some of the changes. 

The major changes are:
o Implement parallel computing stuff
o Implement mixed model permutation
o Add a new Fs test based on shrinked variance components

The minor changes are:
o modify macluster and consensus for mixed model clustering
o Add a new pooled permutation P value (per gene) in ftest

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Version 0.92-1 3/12/2003

o Fix bugs in makeModel, fitmaanova to take null model (y~1)

o Add function bioc2maanova and maanova2bioc

o fix a bug in caldf (the function to calcualte degree of freedom in a test)

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Version 0.91-3 2/6/03

Major changes:

o New function geneprofile to plot expression level for selected genes.

o Output the indices for all three F 

o Output tabulated P values (in Chi2) for F2 and F3 in ftest.fixed.

o Modify volcano, add options for choosing 5 different P values 
in all 3 F tests.

o fix a bug in ftest (for sample permutation)

o covariate is implemented. Covariate will be a continuous variable
functions makeModel, fitmaanova, ftest are changed.

o fix a bug in fitmaanova, e.g., if there's no enough df for fitting,
issue error msg and stop. In mixed model fitting, if there's no enough
df for corresponding fixed model in variance components calculation,
skip it and use default initial value for variances.

Minor changes:

o Fix a bug in write.madata (nreps=1 for rawdata)

o Fix a bug in smooth (shift for rawdata)

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Version 0.91-1 1/9/03

Major changes:

o Implement mixed model ANOVA

o Seperate AG to AG and SG

o Make new function gridcheck for quality check

o Make new function test.Contrast fot t test in mixed model

Minor changes:

o rename make.CI to boot.CI

o rename make.Ftest to ftest

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Version 0.8-2, 9/30/02
Minor changes:
o fix bug in makeModel() for uneven experimental design.

Version 0.8-1, 6/12/02
Major change(s):

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Version 0.6-4, 12/27/01

Major change(s):

o Add make.bayesian() to implement Lonnstedt and Speed's idea.
  (without man page. This function could be buggy)

Minor changes:

o Correct bugs in subset.madata

o Correct bugs in shift(), method LOWESS

o Add read.spotfinder() function to read data from TIGR's spotfind output.

o Add make.cleandata() function to clean the data from TIGR's spotfinder

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Version 0.6-3, 12/19/01

Minor changes:

o Correct bugs in makeFtest.c for multi-replicate case

o Correct bugs in createData (line 36, fixed field is "metarow"
  instead of "metaraw")

o Write dbldyeflip.R for demonstration


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Version 0.6-2, 12/11/01

Minor changes:

o Modified make.Ftest() to take multiple significant levels.

o Modified make.CI() to take multiple significant levels.

Note:

o Rewrite shift in C, done but didn't improve the performance much.
  R version will be kept.

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Version 0.6-1, 12/8/01

Major changes:

o Add function arrayview() to visualize the data on slides

o Add function volcano() to do volcano plot for flip dye experiments

o Add function make.ratio() to calculate the log ratio for raw data

o Add function Simulation() to generate the simulated data

o Add function subset.madata() to subset the madata object

o Add "lowess" as a method to do data shift in shift() function

o Add one option avgreps in createData() to average the replicates.

o Modify the madata data structure, add metarow, metacol, row and col
  as required fields. If these values are not provided, default value
  will be set. Made corresponding changes in read.madata() and 
  createdata() functions.
  

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Version 0.5-1, 12/3/01

Initial release. Software contains most of the functions in Matlab
version of MAANOVA. Here's a list of the functions

o createData
o fitmaanova
o make.CI
o make.Ftest
o makeModel
o read.madata
o resiplot
o riplot
o shift
o summary.madata
o summary.mamodel


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copyright (c) 2001-2004, Hao Wu, The Jackson Laboratory
Licensed under the GNU General Public License version 2 (June, 1991)
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end of STATUS.txt


