Package 'oligo' - Bioconductor

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24 oligo-defunctExamples## How pm() works## Not run:x
oligoPLM-class 25ArgumentsDetails... Arguments.fitPLM was replaced by fitProbeLevelModel, allowing faster execution and providing morespecific models. fitPLM was based in the code written by Ben Bolstad in the affyPLM package.However, all the model-fitting functions are now in the package preprocessCore, on whichfitProbeLevelModel depends.coefs and resids, like fitPLM, were inherited from the affyPLM package. They were replacedrespectively by coef and residuals, because this is how these statistics are called everywhere elsein R.oligoPLM-classClass "oligoPLM"DescriptionA class to represent Probe Level Models.Objects from the ClassSlotsObjects can be created by calls of the form fitProbeLevelModel(FeatureSetObject), whereFeatureSetObject is an object obtained through read.celfiles or read.xysfiles, representingintensities observed for different probes (which are grouped in probesets or meta-probesets) acrossdistinct samples.chip.coefs: "matrix" with chip/sample effects - probeset-levelprobe.coefs: "numeric" vector with probe effectsweights: "matrix" with weights - probe-levelresiduals: "matrix" with residuals - probe-levelse.chip.coefs: "matrix" with standard errors for chip/sample coefficientsse.probe.coefs: "numeric" vector with standard errors for probe effectsresidualSE: scale - residual standard errorgeometry: array geometry used for plotsmethod: "character" string describing method used for PLMmanufacturer: "character" string with manufacturer nameannotation: "character" string with the name of the annotation packagenarrays: "integer" describing the number of arraysnprobes: "integer" describing the number of probes before summarizationnprobesets: "integer" describing the number of probesets after summarization
Page 1 and 2: Package ‘oligo’May 22, 2014Vers
Page 3 and 4: oligo-package 3snprma . . . . . . .
Page 5 and 6: asicRMA 5ValueA list with the follo
Page 7 and 8: chromosome 7DetailsThe ’transfo
Page 9 and 10: darkColors 9darkColorsCreate set of
Page 11 and 12: getAffinitySplineCoefficients 11See
Page 13 and 14: getCrlmmSummaries 13getCrlmmSummari
Page 15 and 16: getPlatformDesign 15getPlatformDesi
Page 17 and 18: hist 17Examples## Not run:x
Page 19 and 20: justSNPRMA 19justSNPRMASummarizatio
Page 21 and 22: MAplot 21groups, refSamples, which,
Page 23: mmindex 23DetailsFor all objects bu
Page 27 and 28: paCalls 27Examples## TODO: review c
Page 29 and 30: plotM-methods 29head(dabgP) ## for
Page 31 and 32: pmStrand 31ArgumentsobjectAffySNPPD
Page 33 and 34: ead.xysfiles 33DetailsWhen using
Page 35 and 36: eadSummaries 35readSummariesRead su
Page 37 and 38: unDate 37ReferencesRafael. A. Iriza
Page 39 and 40: summarize 39ArgumentsValueobjectSnp
Page 41 and 42: Index∗Topic IOread.celfiles, 32re
Page 43 and 44: INDEX 43manufacturer,oligoPLM-metho
Page 45: INDEX 45runDate-methods (runDate),

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