NEWS

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affy 1.41.1

• Fixed bug. attr(r,"constant") <- thisconstant * refconstant to attr(r,"constant") <- refconstant / thisconstant. Reported Aris Floratos.

affy 1.23

• Populate new eSet slot 'protocolData' with information from cel files.

affy 1.17

• Replaced usage of defunct Biobase classes exprSet and phenoData with ExpressionSet and AnnotatedDataFrame.

affy 1.4

• xy2indices/indices2xy have now a (dangerous) parameter xy.offset. See below for more details.
• 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.
• 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)
• indexProbes (method of AffyBatch) sees the deprecated flag 'xy' removed for good.
• mmindex (see indexProbes above)
• pmindex (see indexProbes above)
• 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).
• rma - the subset parameter now works properly.
• 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.

affy 1.3

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

• More consistent usage/application of MIAME

affy 1.2

• Autoload of cdfenvs on demand (uses reposTools). Can be configured through the options.
• 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]
• 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].
• tuning of the MAS5.0 methods implemented (bgcorrect.mas, ...) [Ben for details. add URL for the comparison he made]
• method plot.ProbeSet, an alternative to barplot, to plot probe level information.
• parameter 'scale' in the method barplot for ProbeSet. All the barplots are scaled to eachothers.This is the default.
• bug in the parser fixed (infinite loop reported with apparently non-standard CEL files.).
• bug in the parser fixed (the 'sd' data returned were not correct).
• missing slot in the dataset SpikeIn fixed.
• 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.
• bug in normalize.AffyBatch.qspline fixed (thanks to people at Insightful). The expression data matrix sent to normalize.qspline was mistakingly transposed.
• The default background on the rma() function has been changed. Now the results from rma() and expresso() should agree completely.
• New functions 'xy2indices' and 'indices2xy' to shuttle from x/y pos to indices (like the ones in cdfenvs) (and reverse).
• Reformating of the documentation.

affy 1.1

• 'image(cel)' scales to the size (# rows and # cols) of a chip. locations can be plotted over directly ('plotLocations' was fixed accordiginly).
• 'write.celfile(cel)' to write Cel objects into .CEL files
• 'getInfoInAffyFile' to snoop in CEL and CDF files
• 'whatcdf' to get the name of the CDF from the CEL
• one more slot in class 'Cdf': cdfName (will match with what is returned by 'whatcdf')
• one more slot in class 'Cel': cdfName (returned by whatcdf)
• new class 'AffyBatch': cdfName (returned by whatcdf)
• extensive set of tests in the directory 'tests/'