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gcrma Return Values Description ExpressionMatrix Matrix of log2 expression values where each row corresponds to a gene (probe set) and each column corresponds to an Affymetrix CEL file, which represents a single chip. ExpressionMatrix = gcrma(PMMatrix, MMMatrix, ProbeIndices, AffinPM, AffinMM) performs GCRMA background adjustment, quantile normalization , and median-polish summarization on Affymetrix microarray probe-level data using probe affinity data. ExpressionMatrix is a matrix of log2 expression values where each row corresponds to a gene (probe set) and each column corresponds to an Affymetrix CEL file, which represents a single chip. Note There is no column in ExpressionMatrix that contains probe set or gene information. ExpressionMatrix = gcrma(PMMatrix, MMMatrix, ProbeIndices, SequenceMatrix) performs GCRMA background adjustment, quantile normalization, and Robust Multi-array Average (RMA) summarization on Affymetrix microarray probe-level data using probe sequence data to compute probe affinity data. ExpressionMatrix is a matrix of log2 expression values where each row corresponds to a gene (probe set) and each column corresponds to an Affymetrix CEL file, which represents a single chip. Note If AffinPM and AffinMM affinity data and SequenceMatrix sequence data are not available, you can still use the gcrma function by entering an empty matrix for these inputs in the syntax. ExpressionMatrix = gcrma( ...'PropertyName', PropertyValue, ...) calls gcrma with optional properties that use property 2-164
