Logical, should spots with zero or negative weights be plotted? If NULL, then all points are plotted in the default color, symbol and size. Vector giving the control status of each spot on the array, of same length as the number of rows of object. If specified, then column is ignored.Īlternative to column for fitted model objects. )Īn RGList, MAList, EList, ExpressionSet or MArrayLM object.Īlternative to column for microarray data objects. ) # S3 method for class 'MArrayLM' plotMD ( object, column = ncol ( object ), coef = NULL, xlab = 'Average log-expression', ylab = 'log-fold-change', main = colnames ( object ), status = object $ genes $ Status, zero.weights = FALSE. ) # S3 method for class 'MAList' plotMD ( object, column = 1, array = NULL, xlab = 'A', ylab = 'M', main = colnames ( object ), status = object $ genes $ Status, zero.weights = FALSE. ) # S3 method for class 'RGList' plotMD ( object, column = 1, array = NULL, xlab = 'A', ylab = 'M', main = colnames ( object ), status = object $ genes $ Status, zero.weights = FALSE. ) # S3 method for class 'EList' plotMD ( object, column = 1, array = NULL, xlab = 'Average log-expression', ylab = 'Expression log-ratio (this sample vs others)', main = colnames ( object ), status = object $ genes $ Status, zero.weights = FALSE. # Default S3 method: plotMD ( object, column = 1, xlab = 'Average log-expression', ylab = 'Expression log-ratio (this sample vs others)', main = colnames ( object ), status = NULL. 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.

Malist meaning