Index vector specifying which rows (probes) of y are in the test set.Ĭan be a vector of integer indices, or a logical vector of length nrow(y), or a vector of gene IDs corresponding to entries in geneid.Īlternatively it can be a ame with the first column containing the index vector and the second column containing directional gene contribution weights.įor mroast or fry, index is a list of index vectors or a list of ames.Ĭan be an integer specifying a column of design, or the name of a column of design, or a numeric contrast vector of length equal to the number of columns of design. 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. 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.
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