If both prior parameters are given, then only y values for the test set are required. If either var.prior or df.prior are NULL, then y should contain values for all genes on the arrays. Rows correspond to probes and columns to samples.
#Malist meaning series#
Numeric matrix giving log-expression or log-ratio values for a series of microarrays, or any object that can coerced to a matrix including ExpressionSet, MAList, EList or PLMSet objects. ) # Default S3 method: fry ( y, index = NULL, design = NULL, contrast = ncol ( design ), geneid = NULL, gene.weights = NULL, standardize = "posterior.sd", sort = "directional". ) # Default S3 method: mroast ( y, index = NULL, design = NULL, contrast = ncol ( design ), geneid = NULL, set.statistic = "mean", gene.weights = NULL, var.prior = NULL, df.prior = NULL, nrot = 1999, approx.zscore = TRUE, legacy = FALSE, thod = "BH", midp = TRUE, sort = "directional". # Default S3 method: roast ( y, index = NULL, design = NULL, contrast = ncol ( design ), geneid = NULL, set.statistic = "mean", gene.weights = NULL, var.prior = NULL, df.prior = NULL, nrot = 1999, approx.zscore = TRUE, legacy = FALSE. fitfdist: Moment Estimation of Scaled F-Distribution.exprsMA: Extract Log-Expression Matrix from MAList.ebayes: Empirical Bayes Statistics for Differential Expression.dimnames: Retrieve the Dimension Names of an RGList, MAList, EList.dim: Retrieve the Dimensions of an RGList, MAList or MArrayLM.diffSplice: Test for Differential Splicing.detectionPValue: Detection P-Values from Negative Controls.decideTests: Multiple Testing Across Genes and Contrasts.cumOverlap: Cumulative Overlap Analysis of Ordered Lists.coolmap: Heatmap of gene expression values.controlStatus: Set Status of each Spot from List of Spot Types.contrasts.fit: Compute Contrasts from Linear Model Fit.
contrastAsCoef: Reform a Design Matrix to that Contrasts Become Coefficients.classifytestsF: Genewise Nested F-Tests.chooseLowessSpan: Choose Span for Local-Weighted Regression Smoothing.channel2M: Convert Individual Channel Design Matrix to M-A Format.cbind: Combine RGList, MAList, EList or EListRaw Objects.camera: Competitive Gene Set Test Accounting for Inter-gene.bwss.matrix: Between and within sums of squares for matrix.bwss: Between and within sums of squares.beadCountWeights: Bead Count Weights for Illumina BeadChips.backgroundcorrect: Correct Intensities for Background.avereps: Average Over Irregular Replicate Probes.avearrays: Average Over Replicate Arrays.auROC: Area Under Receiver Operating Curve.asmatrix: Turn a Microarray Data Object into a Matrix.asmalist: Convert marrayNorm Object to an MAList Object.asdataframe: Turn a Microarray Linear Model Object into a Dataframe.arrayWeightsQuick: Array Quality Weights.alias2Symbol: Convert Gene Aliases to Official Gene Symbols.11RNAseq: Topic: Analysis of RNA-seq Data.09Diagnostics: Topic: Diagnostics and Quality Assessment.08Tests: Topic: Hypothesis Testing for Linear Models.07SingleChannel: Topic: Individual Channel Analysis of Two-Color Microarrays.06linearmodels: Topic: Linear Models for Microarrays.05Normalization: Topic: Normalization of Microarray Data.04Background: Topic: Background Correction.03reading: Topic: Reading Microarray Data from Files.02classes: Topic: Classes Defined by this Package.01Introduction: Introduction to the LIMMA Package.
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