The use of within-array replicate spots for assessing differential expression in microarray experiments. Numeric vector of length nrow(object)/ndups giving the individual genewise atanh-transformed correlations.
MALIST MEANING SOFTWARE
Same as rrelation, for compatibility with earlier versions of the software The average is the trimmed mean of the individual correlations on the atanh-transformed scale. The average estimated inter-duplicate correlation. The consensus estimator computed by this function will not be materially affected by a small number of genes. This is not a serious concern providing that there are only a few such warnings and the total number of genes is large. It is not uncommon for the function to return a small number of warning messages that correlation estimates cannot be computed for some individual genes. The function may take long time to execute as it fits a mixed linear model for each gene for an iterative algorithm. If block is not null, then the function will set ndups=1, which is equivalent to ignoring duplicate spots.įor this function to return statistically useful results, there must be at least two more arrays than the number of coefficients to be estimated, i.e., two more than the column rank of design. The function also returns a consensus correlation, which is a robust average of the individual correlations, which can be used as input forĪt this time it is not possible to estimate correlations between duplicate spots and between technical replicates simultaneously. In either case, the correlation is estimated by fitting a mixed linear model by REML individually for each gene. Typically the blocks are biological replicates and the repeated observations are technical replicates. If block is not null, this function estimates the correlation between repeated observations on the blocking variable. When block=NULL, this function estimates the correlation between duplicate spots (regularly spaced within-array replicate spots). If smaller than object then it will be filled out the same size.
The fraction of observations to be trimmed from each end of tanh(all.correlations) when computing the trimmed mean.Īn optional numeric matrix of the same dimension as object containing weights for each spot. Vector or factor specifying a blocking variable The spacing between the rows of object corresponding to duplicate spots, spacing=1 for consecutive spots
Defaults to the unit vector meaning that the arrays are treated as replicates.Ī positive integer giving the number of times each gene is printed on an array. The number of rows must match the number of columns of object. The design matrix of the microarray experiment, with rows corresponding to arrays and columns to comparisons to be estimated. Specifying these arguments explicitly will over-rule any components found in the data object. If object is an MAList object then the arguments design, ndups, spacing and weights will be extracted from it if available and do not have to be specified as arguments.
MALIST MEANING SERIES
R: Correlation Between Duplicates dupcor Ĭorrelation Between Duplicates DescriptionĮstimate the correlation between duplicate spots (regularly spaced replicate spots on the same array) or between technical replicates from a series of arrays.ĭuplicateCorrelation(object, design=NULL, ndups=2, spacing=1, block=NULL,Ī numeric matrix of expression values, or any data object from which as.matrix will extract a suitable matrix such as an MAList, marrayNorm or ExpressionSet object.
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