Package 'oligo' - Bioconductor

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6 boxplotArgumentspmMatMatrix of intensities to be processed.pnVecProbeset names.normalize Logical flag: normalize?background Logical flag: background adjustment?bgversion Version of background correction.destructive Logical flag: use destructive methods?verbose Logical flag: verbose.... Not currently used.ValueMatrix.Examplesset.seed(1)pms
chromosome 7DetailsThe ’transfo’ argument will set the transformation to be used. For raw data, ’transfo=log2’ is acommon practice. For summarized data (which are often in log2-scale), no transformation is needed(therefore ’transfo=identity’).NoteThe boxplot methods for FeatureSet and Expression use a sample (via sample) of the probes/probesetsto produce the plot. Therefore, the user interested in reproducibility is advised to use set.seed.See Alsohist, image, sample, set.seedchromosomeAccessor for chromosome informationDescriptionReturns chromosome information.UsagepmChr(object)ArgumentsobjectTilingFeatureSet or SnpCallSet objectDetailschromosome() returns the chromosomal information for all probes and pmChr() subsets the outputto the PM probes only (if a TilingFeatureSet object).ValueVector with chromosome information.
Page 1 and 2: Package ‘oligo’May 22, 2014Vers
Page 3 and 4: oligo-package 3snprma . . . . . . .
Page 5: asicRMA 5ValueA list with the follo
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 and 24: mmindex 23DetailsFor all objects bu
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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