This function summarizes the replicate values stored in slot
assayData of a
and calculates a single score for each probe. Data are stored in slot
assayData overridding its current content.
This function is implemented for single- and multi-channel data.
an object of class
a character string indicating how to summarize between replicate measurements. One of "min" (default), "mean", "median", "max", "rms", "closestToZero", or "FurthestFromZero" can be used (see details).
A single value per probe is calculated by summarizing between scored replicates stored in the slot
object. The summary is performed as follows:
summary="mean", the average of replicate values is considered;
summary="median", the median of replicate values is considered;
summary="max", the maximum of replicate intensities is taken;
summary="min", the minimum is considered, instead;
summary="rms", the square root of the mean squared value of the replicates (root mean square) is taken as a summary function;
summary="closestToZero", the value closest to zero is taken as a summary (useful when both sides of the distribution of z-score values are of interest);
summary="furthestFromZero", the value furthest from zero is taken as a summary (useful when both sides of the distribution of z-score values are of interest).
cellHTS object with the summarized scored values stored in slot
assayData. This is an object of class
assayData corresponding to matrices of dimensions Features x 1 for each channel.
Moreover, the processing status of the
cellHTS object is updated
in the slot
[email protected][["scored"]]= TRUE.
Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.
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data(KcViabSmall) # normalize x <- normalizePlates(KcViabSmall, scale="multiplicative", method="median", varianceAdjust="none") # score the replicates x <- scoreReplicates(x, sign="-", method="zscore") # summarize the replicates (conservative approach: take the minimum value between replicates) x <- summarizeReplicates(x, summary="min")
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