AffyExtensions - Older versions

What?

Older versions of the package AffyExtensions which contains a set of routines that can be called from within R.

Version 0.3 series requires affy (Version 1.0.2) and bioconductor 1.0 release
Linux/Unix and the like	Windows
AffyExtensions_0.3-3.tar.gz	AffyExtensions_0.3-3.zip

Version 0.4 series requires affy (Bioconductor 1.1 release)
Linux/Unix and the like	Windows	Date	Comments
Versions 0.4-1 through 0.4-14 are available upon request here
AffyExtensions_0.4-15.tar.gz	AffyExtensions_0.4-15.zip	Feb 27, 2003	Incremental updates. Slightly longer vignette. Except for bug fixes, the last release in the 0.4 series

Version 0.5 series requires affy (Bioconductor 1.2 release)
Linux/Unix and the like	Windows	Date	Comments
Versions 0.5-0 through 0.5-13 are available upon request here
AffyExtensions_0.5-14.tar.gz	AffyExtensions_0.5-14.zip	Sep 12, 2003	Fix a bug in how constraints are applied

Version 0.6 series requires affy (Bioconductor 1.3) package. Note that 0.6 is the development series
AffyExtensions_0.6-4.tar.gz	Not currently available	Jan 12, 2004	PLM.tstat introduced
AffyExtensions_0.6-5.tar.gz	AffyExtensions_0.6-5.zip	Mar 13, 2004	Interaction style terms can now be specified in model for fitPLM
AffyExtensions_0.6-6.tar.gz	Not currently available	Apr 29, 2004	PLM.tstat/PLM.fstat introduced
AffyExtensions_0.6-7.tar.gz	Not currently available	May 24, 2004	Fixed some memory leaks. Compatible with BioC 1.4 and R 1.9.X

Longer history of changes for current (0.6) series

Version	Date of Release	Comments
0.6-0	Never released publically (only available to UCB)	the PLMset object now has new attributes residuals - a matrix storing residuals from model fit (notice that these are normalization vector -vector (in sorted order of PM probe intensities for normalization distribution) DESCRIPTION item is now a list, that can be used more carefully to describe how the model was fit residual standard error and df varcov - variance covariance matrices for each model "residuals", residual SE, varcov are returned in the PLMset object returned from fitPLM (depending on user flags). image() on a PLMset can now plot residuals and possible to add legend bars. Some major changes in how parameters are passed in some of the C code routines in the fitPLM process (this should not be of consequence to the user) boxplot function for exprSets normalize.exprSet.invariantset - now has same choices of baselines as in the affy package. conversion function pset2eset() which converts a PLMset to an exprSet fitPLM now has parameters output.param and model.param which are lists. It allows the user better control over how model is fit and what is outputted. rmaPLM() function lets you fit the rma model as a PLMset. This allows you to use the image function on residuals. threestep() now has a summary.param parameter which gives you some control over the summarization routines. threestepPLM() function returns residuals in addition to expression values in a PLMset
0.6-1	Oct 18, 2003	Preliminary support for binary CEL files. Note that this package works with Release 1.2 bioconductor and R-1.7.1
0.6-2	Nov 20, 2003	Minor fixes. Support for R-1.8.0 and Release 1.3 Bioconductor
0.6-3	Dec 8, 2003	Remove all cel file parsing code. This is now in the base affy package (1.4.3 or later). Replacement functions for residuals/resid.
0.6-4	Jan 12, 2004	sampleNames replacement function for PLMset objects weights/residuals allow you to index probes from specific probesets resid/residuals functions allow you to choose standardized residuals a general test statistic function PLM.tstat
0.6-5	Mar 13, 2004	Change how kappa is computed in SE algorithm (this affects non-Huber psi fns) threestep,rmaPLM,threestepPLM,fitPLM - accept the subset parameter which allowing you to restrict computations to a set of specified probesets. MAplot() function gives n MA plots equivalent to Mbox() Interaction style terms can now be specified in model for fitPLM
0.6-6	Apr 29, 2004	PLM.tstat has been updated. PLM.fstat introduced Some of the man/ documentation has been cleaned up A function PLM.flags() has been introduced
0.6-7	May 24, 2004	Fixed some memory leaks. Compatible with BioC 1.4 and R 1.9.X

Longer history of changes for 0.5 series

Version	Date of Release	Comments
0.5-0	Mar 27, 2003	Initial Release. New background methods (not default), ability to do MAS like background. Only version of the 0.5 series that will work with versions of R earlier than R-1.7.0
0.5-1	May 13, 2003	Requires R-1.7.x and affy version 1.2.19 or later. This means the package should work well with the forthcoming Bioconductor 1.2 release. The default background method in fitPLM and threestep has been changed so that it agrees with affy. Note that some lapack routines are now used internally in preference to linpack.
0.5-2	May 30, 2003	Another normalization method called quantiles.probeset. Currently it is a separate function, it will be integrated into threestep() and fitPLM() at a later point.
0.5-3	Jun 11, 2003	Other M estimation Psi functions have been added to fitPLM(). These may be specified using the psi.type parameter. (An additional parameter psi.k controls a tuning parameter). Currently iteration of all of these methods is started at the ordinary linear regression estimates.
0.5-4	Jun 12, 2003	A function callPA was introduced. It makes Presence/Absence calls. Note that this is not the same method used by the MAS 5.0 software
0.5-5	Jun 15, 2003	First version of read.affybatch2. It is designed to be faster with large numbers of chips. Overload your read.affybatch by using read.affybatch <- read.affybatch2 to use it with ReadAffy()
0.5-6	Jun 17, 2003	Modifications to read.affybatch2. It now deals with OUTLIER and MASKS sections if required. Windows build uses R-1.7.1
0.5-7	Jun 19, 2003	Modifications to read.affybatch2. This should cut a little more time off the run time of this routine.
0.5-8	Jun 24, 2003	You can now call "quantile.probeset" as a normalization method in threestep(), fitPLM()
0.5-9	Jul 19, 2003	Mbox function. Note that the parsing routines are now also available in the affy devel packages.
0.5-10	Jul 19, 2003	fix error in how constraints are applied.
0.5-11	Aug 20, 2003	SE are now outputed from some threestep methods. Reduce memory overhead in threestep. Fix a bunch of compiler warnings (all were not fatal) that have not been worked on previously. A vignette describing the threestep function. Changes to how options to background and normalization methods are handled in threestep/fitPLM. normalize.AffyBatch.quantiles.probeset can deal with MM values. callPA() has been modified, it provides more options.
0.5-12	Aug 26, 2003	Normalization routines for exprSets. There is now a generic function normalize() that may be applied to exprSets in the same manner as AffyBatches. A function for doing the scaling normalization added (differs slightly from normalize.constant in that pseudo baseline chips may be used and a trimmed mean might be used). can call via normalize.AffyBatch.scaling, normalize() changed normalize.quantiles.probeset so it can now work on natural scale
0.5-13	Aug 28, 2003	fitPLM/threestep can now send proper parameters to quantiles.probeset. a little more control over what happens to an affybatch when you use the scaling normalization.
0.5-14	Sep 12, 2003	There was a bug in how constraints were applied. If the variable was defined in the parent environment then the constraint was not properly applied.

Longer history of changes for 0.4 series

Version	Date of Release	Comments
0.4-0	Jan 9, 2003	Initial Release. Not all background or summary methods included.
0.4-1	Jan 11, 2003	More Summary methods, background methods working. Calling methodology refined
0.4-2	Jan 13, 2003	Introduction of robust linear model in threestep method.
0.4-3	Jan 22, 2003	Introduction of PLMset object. fitPLM() function introduced, only fits default model
0.4-4	Jan 23, 2003	Ability to make image plots of the weights
0.4-5	Jan 27, 2003	Wider set of models may be fitted. First pass attempt at standard errors.
0.4-6	Jan 28, 2003	Better attempts at standard errors. Please add se.type=4 to your fitPLM calls, default se.type is numerically unstable
0.4-7	Jan 30, 2003	Fix to se.type=4 (which has become the default type). Distinct row names on weights matrix (to allow write.table to work better). A boxplot type function for PLMset objects
0.4-8	Feb 2, 2003	Fix so that se.type=2 and se.type=3 should work properly now (numerical instability removed). Some slight optimizations.
0.4-9	Feb 6, 2003	Incremental updates to fitPLM. A vignette. Four new summary methods in threestep.
0.4-10	Feb 9, 2003	Optimization to se.type=4 in fitPLM. Fuller vignette.
0.4-11	Feb 11, 2003	A number of space, time optimizations. Fix to se.type=1,2,3 (can explain why differ from summary.rlm)
0.4-12	Feb 15, 2003	Incremental updates. Vignette should work with windows build.
0.4-13	Feb 18, 2003	Ability to fit models with intercept coefficients and to fit models with out probe effects. Accessor functions for probe/ intercept parameters
0.4-14	Feb 25, 2003	Ability to fit models with sum to zero constraints. image gives correctly oriented plot.
0.4-15	Feb 27, 2003	Incremental updates. Slightly longer vignette. Except for bug fixes, the last release in the 0.4 series

Older Documentation

Documentation for AffyExtensions (0.3-3) is in this PDF file.

Special Notes

This software as of version (0.3-3) is recommended only for use with affy 1.0.2. Release 1.1 of Bioconductor brings with it a much changed affy package. A fast RMA has been integrated into that release.