Numeric matrix of same dimensions as M containing relative spot quality weights. Numeric matrix containing the A-values (average log-2 expression values). Rows correspond to spots and columns to arrays. Numeric matrix containing the M-values (log-2 expression ratios). Data), but objects should contain the following components: This class contains no slots (other than. MAList objects can be created by new("MAList",MA) where MA is a list. MAList objects are usually created during normalization by the functions normalizeWithinArrays or MA.RG. In limma: Linear Models for Microarray Dataĭescription Slots/List Components Methods Author(s) See AlsoĪ simple list-based class for storing M-values and A-values for a batch of spotted microarrays. 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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