Package 'oligo' - Bioconductor

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22 mmAuthor(s)Benilton Carvalho - based on Ben Bolstad’s original MAplot function.See Alsoplot, smoothScatterExamplesif(require(oligoData) & require(pd.hg18.60mer.expr)){data(nimbleExpressionFS)nimbleExpressionFSgroups
mmindex 23DetailsFor all objects but TilingFeatureSet, these methods will return matrices. In case of TilingFeatureSetobjects, the value is a 3-dimensional array (probes x samples x channels).intensity will return the whole intensity matrix associated to the object. pm, mm, bg will return therespective PM/MM/BG matrix.When applied to ExonFeatureSet or GeneFeatureSet objects, pm will return the PM matrix at thetranscript level (’core’ probes) by default. The user should set the target argument accordingly ifsomething else is desired. The valid values are: ’probeset’ (Exon and Gene arrays), ’core’ (Exonand Gene arrays), ’full’ (Exon arrays) and ’extended’ (Exon arrays).The target argument has no effects when used on designs other than Gene and Exon ST.Examplesif (require(maqcExpression4plex) & require(pd.hg18.60mer.expr)){xysPath
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: MAplot 21groups, refSamples, which,
Page 25 and 26: oligoPLM-class 25ArgumentsDetails..
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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