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Removing Affy tree - which was in there for RMA. Maybe another day.

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1 parent ea4a9b4 commit f17cf2c27449de41d25aea08827b919b6a7b0858 @pjotrp committed Jan 25, 2010
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  1. +0 −38 src/clibs/affy-1.18.2/DESCRIPTION
  2. +0 −141 src/clibs/affy-1.18.2/NEWS
  3. +0 −813 src/clibs/affy-1.18.2/R/AffyBatch.R
  4. +0 −98 src/clibs/affy-1.18.2/R/AffyRNAdeg.R
  5. +0 −135 src/clibs/affy-1.18.2/R/ProbeSet.R
  6. +0 −76 src/clibs/affy-1.18.2/R/ProgressBarText.R
  7. +0 −14 src/clibs/affy-1.18.2/R/avdiff.R
  8. +0 −44 src/clibs/affy-1.18.2/R/barplot.ProbeSet.R
  9. +0 −36 src/clibs/affy-1.18.2/R/bg.Affy.chipwide.R
  10. +0 −76 src/clibs/affy-1.18.2/R/bg.R
  11. +0 −138 src/clibs/affy-1.18.2/R/expresso.R
  12. +0 −119 src/clibs/affy-1.18.2/R/expressoWidget.R
  13. +0 −171 src/clibs/affy-1.18.2/R/fit.li.wong.R
  14. +0 −8 src/clibs/affy-1.18.2/R/generateExprVal.method.avgdiff.R
  15. +0 −11 src/clibs/affy-1.18.2/R/generateExprVal.method.liwong.R
  16. +0 −35 src/clibs/affy-1.18.2/R/generateExprVal.method.mas.R
  17. +0 −3 src/clibs/affy-1.18.2/R/generateExprVal.method.medianpolish.R
  18. +0 −40 src/clibs/affy-1.18.2/R/generateExprVal.method.playerout.R
  19. +0 −175 src/clibs/affy-1.18.2/R/getCDFenv.R
  20. +0 −17 src/clibs/affy-1.18.2/R/hlog.R
  21. +0 −142 src/clibs/affy-1.18.2/R/justrma.R
  22. +0 −45 src/clibs/affy-1.18.2/R/loess.normalize.R
  23. +0 −369 src/clibs/affy-1.18.2/R/maffy.R
  24. +0 −153 src/clibs/affy-1.18.2/R/mas5.R
  25. +0 −36 src/clibs/affy-1.18.2/R/merge.AffyBatch.R
  26. +0 −393 src/clibs/affy-1.18.2/R/mva.pairs.R
  27. +0 −33 src/clibs/affy-1.18.2/R/normalize.constant.R
  28. +0 −38 src/clibs/affy-1.18.2/R/normalize.contrasts.R
  29. +0 −138 src/clibs/affy-1.18.2/R/normalize.invariantset.R
  30. +0 −90 src/clibs/affy-1.18.2/R/normalize.loess.R
  31. +0 −150 src/clibs/affy-1.18.2/R/normalize.qspline.R
  32. +0 −93 src/clibs/affy-1.18.2/R/normalize.quantiles.R
  33. +0 −32 src/clibs/affy-1.18.2/R/pairs.AffyBatch.R
  34. +0 −16 src/clibs/affy-1.18.2/R/plot.ProbeSet.R
  35. +0 −51 src/clibs/affy-1.18.2/R/plot.density.R
  36. +0 −8 src/clibs/affy-1.18.2/R/plotLocation.R
  37. +0 −31 src/clibs/affy-1.18.2/R/pmcorrect.mas.R
  38. +0 −10 src/clibs/affy-1.18.2/R/ppset.ttest.R
  39. +0 −37 src/clibs/affy-1.18.2/R/ppsetApply.R
  40. +0 −309 src/clibs/affy-1.18.2/R/read.affybatch.R
  41. +0 −66 src/clibs/affy-1.18.2/R/rma.R
  42. +0 −55 src/clibs/affy-1.18.2/R/summary.R
  43. +0 −16 src/clibs/affy-1.18.2/R/tukey.biweight.R
  44. +0 −37 src/clibs/affy-1.18.2/R/whatcdf.R
  45. +0 −61 src/clibs/affy-1.18.2/R/xy2indices.R
  46. +0 −139 src/clibs/affy-1.18.2/R/zzz.R
  47. +0 −33 src/clibs/affy-1.18.2/README_BIOLIB
  48. +0 −43 src/clibs/affy-1.18.2/changelog
  49. +0 −14 src/clibs/affy-1.18.2/doc/CITATION
  50. +0 −219 src/clibs/affy-1.18.2/man/AffyBatch-class.Rd
  51. +0 −50 src/clibs/affy-1.18.2/man/AffyRNAdeg.Rd
  52. +0 −51 src/clibs/affy-1.18.2/man/MAplot.Rd
  53. +0 −51 src/clibs/affy-1.18.2/man/ProbeSet-class.Rd
  54. +0 −80 src/clibs/affy-1.18.2/man/ProgressBarText-class.Rd
  55. +0 −35 src/clibs/affy-1.18.2/man/SpikeIn.Rd
  56. +0 −46 src/clibs/affy-1.18.2/man/affy-options.Rd
  57. +0 −29 src/clibs/affy-1.18.2/man/affy.scalevalue.exprSet.Rd
  58. +0 −18 src/clibs/affy-1.18.2/man/affybatch.example.Rd
  59. +0 −34 src/clibs/affy-1.18.2/man/barplot.ProbeSet.Rd
  60. +0 −31 src/clibs/affy-1.18.2/man/bg.adjust.Rd
  61. +0 −75 src/clibs/affy-1.18.2/man/bgc.Rd
  62. +0 −37 src/clibs/affy-1.18.2/man/cdfFromBioC.Rd
  63. +0 −15 src/clibs/affy-1.18.2/man/cdfenv.example.Rd
  64. +0 −44 src/clibs/affy-1.18.2/man/cleancdfname.Rd
  65. +0 −11 src/clibs/affy-1.18.2/man/debug.affy123.Rd
  66. +0 −96 src/clibs/affy-1.18.2/man/expresso.Rd
  67. +0 −59 src/clibs/affy-1.18.2/man/expressoWidget.Rd
  68. +0 −104 src/clibs/affy-1.18.2/man/fit.li.wong.Rd
  69. +0 −58 src/clibs/affy-1.18.2/man/generateExprSet-methods.Rd
  70. +0 −59 src/clibs/affy-1.18.2/man/generateExprVal-methods.Rd
  71. +0 −53 src/clibs/affy-1.18.2/man/generateExprVal.method.avgdiff.Rd
  72. +0 −37 src/clibs/affy-1.18.2/man/generateExprVal.method.playerout.Rd
  73. +0 −26 src/clibs/affy-1.18.2/man/hlog.Rd
  74. +0 −96 src/clibs/affy-1.18.2/man/justrma.Rd
  75. +0 −24 src/clibs/affy-1.18.2/man/list.celfiles.Rd
  76. +0 −44 src/clibs/affy-1.18.2/man/loess.normalize.Rd
  77. +0 −40 src/clibs/affy-1.18.2/man/maffy.normalise.Rd
  78. +0 −32 src/clibs/affy-1.18.2/man/maffy.subset.Rd
  79. +0 −49 src/clibs/affy-1.18.2/man/mas5.Rd
  80. +0 −135 src/clibs/affy-1.18.2/man/mas5calls.Rd
  81. +0 −39 src/clibs/affy-1.18.2/man/merge.AffyBatch.Rd
  82. +0 −29 src/clibs/affy-1.18.2/man/multiloess.Rd
  83. +0 −36 src/clibs/affy-1.18.2/man/mva.pairs.Rd
  84. +0 −66 src/clibs/affy-1.18.2/man/normalize-methods.Rd
  85. +0 −30 src/clibs/affy-1.18.2/man/normalize.Rd
  86. +0 −32 src/clibs/affy-1.18.2/man/normalize.constant.Rd
  87. +0 −32 src/clibs/affy-1.18.2/man/normalize.contrast.Rd
  88. +0 −54 src/clibs/affy-1.18.2/man/normalize.invariantset.Rd
  89. +0 −51 src/clibs/affy-1.18.2/man/normalize.loess.Rd
  90. +0 −84 src/clibs/affy-1.18.2/man/normalize.qspline.Rd
  91. +0 −46 src/clibs/affy-1.18.2/man/normalize.quantiles.Rd
  92. +0 −52 src/clibs/affy-1.18.2/man/normalize.quantiles.robust.Rd
  93. +0 −42 src/clibs/affy-1.18.2/man/pairs.AffyBatch.Rd
  94. +0 −28 src/clibs/affy-1.18.2/man/plot.ProbeSet.Rd
  95. +0 −69 src/clibs/affy-1.18.2/man/plot.density.Rd
  96. +0 −50 src/clibs/affy-1.18.2/man/plotLocation.Rd
  97. +0 −57 src/clibs/affy-1.18.2/man/pmcorrect.Rd
  98. +0 −51 src/clibs/affy-1.18.2/man/ppsetApply.Rd
  99. +0 −18 src/clibs/affy-1.18.2/man/probeMatch-methods.Rd
  100. +0 −17 src/clibs/affy-1.18.2/man/probeNames-methods.Rd
  101. +0 −100 src/clibs/affy-1.18.2/man/read.affybatch.Rd
  102. +0 −44 src/clibs/affy-1.18.2/man/read.probematrix.Rd
  103. +0 −61 src/clibs/affy-1.18.2/man/rma.Rd
  104. +0 −30 src/clibs/affy-1.18.2/man/setAffyOptions.Rd
  105. +0 −27 src/clibs/affy-1.18.2/man/simplemultiLoess.Rd
  106. +0 −19 src/clibs/affy-1.18.2/man/summary.Rd
  107. +0 −28 src/clibs/affy-1.18.2/man/tukey.biweight.Rd
  108. +0 −25 src/clibs/affy-1.18.2/man/whatcdf.Rd
  109. +0 −60 src/clibs/affy-1.18.2/man/xy2indices.Rd
  110. +0 −3 src/clibs/affy-1.18.2/src/Makevars.in
  111. +0 −2 src/clibs/affy-1.18.2/src/Makevars.win
  112. +0 −11 src/clibs/affy-1.18.2/src/biolib_affy.c
  113. +0 −13 src/clibs/affy-1.18.2/src/biolib_affy.h
  114. +0 −536 src/clibs/affy-1.18.2/src/chipbackground.c
  115. +0 −120 src/clibs/affy-1.18.2/src/getall_locations.c
  116. +0 −214 src/clibs/affy-1.18.2/src/mas5calls.c
  117. +0 −404 src/clibs/affy-1.18.2/src/rma2.c
  118. +0 −128 src/clibs/affy-1.18.2/src/rma_common.c
  119. +0 −10 src/clibs/affy-1.18.2/src/rma_common.h
@@ -1,38 +0,0 @@
-Package: affy
-Version: 1.18.2
-Title: Methods for Affymetrix Oligonucleotide Arrays
-Author: Rafael A. Irizarry <rafa@jhu.edu>, Laurent Gautier
- <lgautier@gmail.com>, Benjamin Milo Bolstad
- <bmb@bmbolstad.com>, and Crispin Miller
- <cmiller@picr.man.ac.uk> with contributions from Magnus
- Astrand <Magnus.Astrand@astrazeneca.com>, Leslie M. Cope
- <cope@mts.jhu.edu>, Robert Gentleman, Jeff Gentry, Conrad
- Halling <challing@agilixcorp.com>, Wolfgang Huber, James
- MacDonald <jmacdon@med.umich.edu>, Benjamin I. P. Rubinstein,
- Christopher Workman <workman@cbs.dtu.dk>, John Zhang
-Maintainer: Rafael A. Irizarry <rafa@jhu.edu>
-Depends: R (>= 2.7.0), Biobase (>= 2.0.0), methods, utils, affyio (>= 1.8.0), preprocessCore (>= 1.2.0)
-Suggests: tkWidgets (>= 1.18.0), affydata, geneplotter
-LinkingTo: preprocessCore
-Description: The package contains functions for exploratory
- oligonucleotide array analysis. The dependance to tkWidgets
- only concerns few convenience functions. 'affy' is fully
- functional without it.
-License: LGPL (>= 2.0)
-Collate: ProgressBarText.R ppset.ttest.R ppsetApply.R expressoWidget.R
- getCDFenv.R AffyRNAdeg.R avdiff.R barplot.ProbeSet.R
- bg.Affy.chipwide.R bg.R expresso.R fit.li.wong.R
- generateExprVal.method.avgdiff.R
- generateExprVal.method.liwong.R generateExprVal.method.mas.R
- generateExprVal.method.medianpolish.R
- generateExprVal.method.playerout.R hlog.R justrma.R
- loess.normalize.R maffy.R mas5.R merge.AffyBatch.R
- normalize.constant.R normalize.contrasts.R
- normalize.invariantset.R normalize.loess.R normalize.qspline.R
- normalize.quantiles.R pairs.AffyBatch.R plot.density.R
- plotLocation.R plot.ProbeSet.R pmcorrect.mas.R AffyBatch.R
- mva.pairs.R ProbeSet.R read.affybatch.R rma.R summary.R
- tukey.biweight.R whatcdf.R xy2indices.R zzz.R
-biocViews: Microarray, OneChannel, Preprocessing
-LazyLoad: yes
-Packaged: Fri Jun 13 01:46:16 2008; biocbuild
@@ -1,141 +0,0 @@
-version 1.17.x
-
- o Replaced usage of defunct Biobase classes exprSet and phenoData with
- ExpressionSet and AnnotatedDataFrame.
-
-
-version 1.4.x [under development]
-
- o xy2indices/indices2xy have now a (dangerous) parameter xy.offset.
- See below for more details.
-
- o a new package-wide parameter called 'xy.offset' was added. This is
- the first towards getting rid of the 'indexing-starting-at-one-and
- -not-at-zero' difficulty. This package-wide parameter is the only
- thing one should play play with to change the offset of x/y
- coordinates for features on a chip.
-
- o computeExprSet (method of AffyBatch) has the following (visible)
- improvements:
- - better reporting of errors
- - better handlings ids as parameters (does not crash any longer when
- unknown ids are given)
-
- o indexProbes (method of AffyBatch) sees the deprecated flag 'xy' removed
- for good.
-
- o mmindex (see indexProbes above)
-
- o pmindex (see indexProbes above)
-
- o ppsetApply: a function to apply a function over the probe sets that can be
- built from an instance of AffyBatch. This is done in the spirit of
- esetApply in Biobase (the covariate information in phenoData are
- directly accessible from the function (see example in the man page).
-
- o rma - the subset parameter now works properly.
-
- o mva.pairs - now uses a subset to fit the loess curve (much more efficient).
- also the summary statistics displayed are different. In particular the
- median and IQR of the M's are shown in the lower triangle. Previously,
- an IQR of loess curve values was shown.
-
-
-version 1.3.x
-
-Things done:
-
- 0 (wh:) moved everything related to Cdf-class from 'affy' to 'makecdfenv':
- R/Cdf.R, R/getLocationsData.Cdf.R, locate.name.R, pmormm.R
- R/read.cdffile.R, data/cdf.example.rda, man/Cdf-class.Rd
- man/getLocationsData.Cdf.Rd, man/locate.name.Rd, man/pmormm.Rd
- man/read.cdffile.Rd, src/read_cdffile.c
-
- o read.affybatch2 reads all cel files together in one big hit
- into an affybatch
-
- o the baseline in normalize.AffyBatch,invariant can be selected
- using a baseline.type parameter. Also changed "progress" to the
- more standard "verbose". Seemed to be an error since both PM and
- MM probes were normalized by only PM's where used to establish the
- normalization, now follows same standard as been introduced for
- normalize.AffyBatch.quantiles.
-
- o Most normalization routines can now be called with the parameter
- type which specifies whether to be pmonly, mmonly, both together
- or both separately. This introduces more consistency to the how
- the normalization routines are actually applied to affybatchs.
-
- o express() has been completely removed.
-
-
-Things that would be good to see before next release:
- o More consistent usage/application of MIAME
-
-
-version 1.2.x:
-
- o Autoload of cdfenvs on demand (uses reposTools). Can be
- configured through the options.
-
- o slot 'preprocessing' of the MIAME attribute used to store
- normalization step information [will be polished, list returned
- for the moment. Need for a class and check compliance with MIAME
- standards]
-
- o default methods for normalization, bg correction, pm correction
- and summary now in the package options [options exist for all, but
- only used by normalize for the moment].
-
- o tuning of the MAS5.0 methods implemented (bgcorrect.mas, ...)
- [Ben for details. add URL for the comparison he made]
-
- o method plot.ProbeSet, an alternative to barplot, to plot probe
- level information.
-
- o parameter 'scale' in the method barplot for ProbeSet. All the
- barplots are scaled to eachothers.This is the default.
-
- o bug in the parser fixed (infinite loop reported with apparently
- non-standard CEL files.).
-
- o bug in the parser fixed (the 'sd' data returned were not correct).
-
- o missing slot in the dataset SpikeIn fixed.
-
- o The function express() is deprecated. It still functions normally
- but gives warning mesage. It will be removed in a future release.
- The function expresso() should be used as a replacement.
-
- o bug in normalize.AffyBatch.qspline fixed (thanks to people at
- Insightful). The expression data matrix sent to normalize.qspline
- was mistakingly transposed.
-
- o The default background on the rma() function has been changed. Now
- the results from rma() and expresso() should agree completely.
-
- o New functions 'xy2indices' and 'indices2xy' to shuttle from
- x/y pos to indices (like the ones in cdfenvs) (and reverse).
-
- o Reformating of the documentation.
-
-version 1.1.x:
-
- o 'image(cel)' scales to the size (# rows and # cols) of a chip.
- locations can be plotted over directly ('plotLocations' was fixed
- accordiginly).
-
- o 'write.celfile(cel)' to write Cel objects into .CEL files
-
- o 'getInfoInAffyFile' to snoop in CEL and CDF files
-
- o 'whatcdf' to get the name of the CDF from the CEL
-
- o one more slot in class 'Cdf': cdfName (will match with what is
- returned by 'whatcdf')
-
- o one more slot in class 'Cel': cdfName (returned by whatcdf)
-
- o new class 'AffyBatch': cdfName (returned by whatcdf)
-
- o extensive set of tests in the directory 'tests/'
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