Package 'limma' - Bioconductor

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20 as.data.frame Author(s) Gordon Smyth References Ritchie, M. E., Diyagama, D., Neilson, van Laar, R., J., Dobrovic, A., Holloway, A., and Smyth, G. K. (2006). Empirical array quality weights for microarray data. BMC Bioinformatics. (Accepted 11 April 2006) See Also See arrayWeights. An overview of LIMMA functions for reading data is given in 03.ReadingData. Examples ## Not run: fit
as.MAList 21 Value A data.frame. Author(s) See Also Gordon Smyth as.data.frame in the base package. 02.Classes gives an overview of data classes used in LIMMA. 06.LinearModels gives an overview of linear model functions in LIMMA. as.MAList Convert marrayNorm Object to an MAList Object Description Convert marrayNorm Object to an MAList Object Usage as.MAList(object) Arguments object an marrayNorm object Details Value The marrayNorm class is defined in the marray package. This function converts a normalized two color microarray data object created by the marray package into the corresponding limma data object. Note that such conversion is not necessary to access the limma linear modelling functions, because lmFit will operate on a marrayNorm data object directly. Object of class MAList Author(s) See Also Gordon Smyth 02.Classes gives an overview of all the classes defined by this package.
Page 1 and 2: Package ‘limma’ May 22, 2014 Ve
Page 3 and 4: R topics documented: 3 heatdiagram
Page 5 and 6: 01.Introduction 5 voom . . . . . .
Page 7 and 8: 03.ReadingData 7 03.ReadingData Top
Page 9 and 10: 05.Normalization 9 05.Normalization
Page 11 and 12: 06.LinearModels 11 Assessing Differ
Page 13 and 14: 09.Diagnostics 13 Gene Set Tests Co
Page 15 and 16: 11.RNAseq 15 11.RNAseq Topic: Analy
Page 17 and 18: arrayWeights 17 Arguments Details o
Page 19: arrayWeightsQuick 19 See Also An ov
Page 23 and 24: asMatrixWeights 23 asMatrixWeights
Page 25 and 26: avearrays 25 Examples auROC(c(1,1,0
Page 27 and 28: avereps 27 Author(s) Gordon Smyth S
Page 29 and 30: ackgroundCorrect 29 printer a list
Page 31 and 32: arcodeplot 31 Arguments index index
Page 33 and 34: eadCountWeights 33 Details Value Th
Page 35 and 36: wss 35 Examples a
Page 37 and 38: camera 37 camera Competitive Gene S
Page 39 and 40: cbind 39 Examples y
Page 41 and 42: classifyTests 41 See Also 01.Introd
Page 43 and 44: contrastAsCoef 43 contrastAsCoef Re
Page 45 and 46: contrasts.fit 45 Warning. For effic
Page 47 and 48: decideTests 47 Author(s) Gordon Smy
Page 49 and 50: diffSplice 49 Details Value If desi
Page 51 and 52: dim 51 dim Retrieve the Dimensions
Page 53 and 54: dupcor 53 dupcor Correlation Betwee
Page 55 and 56: ebayes 55 ## End(Not run) ebayes Em
Page 57 and 58: ebayes 57 F F.p.value numeric vecto
Page 59 and 60: exprs.MA 59 See Also 02.Classes giv
Page 61 and 62: fitGammaIntercept 61 References Smy
Page 63 and 64: genas 63 Author(s) Gordon Smyth See
Page 65 and 66: geneSetTest 65 Examples # Simulate
Page 67 and 68: geneSetTest 67 There are four possi
Page 69 and 70: getLayout 69 Author(s) Gordon Smyth
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gls.series 71 Details "rows" means
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gridr 73 Author(s) Gordon Smyth See
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helpMethods 75 Details Value Users
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imageplot 77 zlim mar legend numeri
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intraspotCorrelation 79 intraspotCo
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isNumeric 81 Author(s) Gordon Smyth
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LargeDataObject-class 83 Author(s)
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lm.series 85 lm.series Fit Linear M
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lmFit 87 Details Value This functio
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lmscFit 89 # Suppose two side-by-si
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loessFit 91 Arguments y x weights s
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ma3x3 93 ma3x3 Two dimensional Movi
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makeUnique 95 Examples makeContrast
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MArrayLM-class 97 MArrayLM-class Mi
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merge 99 See Also An overview of di
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mergeScans 101 Value are affected b
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modifyWeights 103 Author(s) Gordon
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nec 105 Details This is a utility f
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normalizeBetweenArrays 107 Referenc
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normalizeBetweenArrays 109 same emp
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normalizeCyclicLoess 111 Details Th
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normalizeForPrintorder 113 Details
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normalizeQuantiles 115 Examples M
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normalizeVSN 117 Value Numeric vect
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normalizeWithinArrays 119 Usage nor
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normexp.fit 121 normexp.fit Fit Nor
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normexp.fit.control 123 Usage norme
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normexp.fit.detection.p 125 Details
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plot.MArrayLM 127 References Ritchi
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plotDensities 129 References See Al
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plotFB 131 plotFB FB-Plot Descripti
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plotMA 133 plotMA MA-Plot Descripti
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plotMA3by2 135 # Same as above attr
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plotMDS 137 Details Value This func
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plotRLDF 139 plotRLDF Plot of regul
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plotSplice 141 Arguments fit xlab y
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predFCm 143 Value A list with compo
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printHead 145 # fit a linear model
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printorder 147 printorder Identify
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printtipWeights 149 Details Value T
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propTrueNull 151 References Shi, W,
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protectMetachar 153 # True pi0 160/
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QualityWeights 155 See Also qqnorm
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ankSumTestWithCorrelation 157 Detai
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ead.idat 159 Author(s) Gordon Smyth
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ead.ilmn 161 ctrlpath probeid annot
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ead.maimages 163 Author(s) Wei Shi
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ead.maimages 165 Value ArrayVision
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eadGAL 167 readGAL Read a GAL file
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eadImaGeneHeader 169 Value A list w
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eadTargets 171 Arguments file path
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emoveExt 173 Arguments x batch batc
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RGList-class 175 RGList-class Red,
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oast 177 array.weights weights bloc
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omer 179 References Goeman, JJ, and
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omer 181 down test. This improves t
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squeezeVar 183 See Also An overview
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strsplit2 185 Sartor MA, Tomlinson
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summary 187 Details i,j may take an
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targetsA2C 189 Value list of intege
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tmixture 191 Author(s) See Also Gor
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topSplice 193 Examples # See romer
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toptable 195 lfc Details confint mi
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tricubeMovingAverage 197 tricubeMov
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trimWhiteSpace 199 trimWhiteSpace T
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venn 201 Value A matrix containing
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volcanoplot 203 volcanoplot Volcano
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vooma 205 Value counts across all s
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weighted.median 207 weighted.median
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write.fit 209 Value A list of numer
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zscore 211 Arguments q, x numeric v
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Index ∗Topic IO controlStatus, 46
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INDEX 215 ma3x3, 93 tricubeMovingAv
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INDEX 217 mergeScans, 100 mergeScan
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INDEX 219 weighted.median, 207 weig
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