summarizeReplicates {cellHTS2} | R Documentation

## Summarize between scored replicate values given in a cellHTS object to obtain a single value for each probe

### Description

This function summarizes the replicate values stored in slot `assayData` of a `cellHTS` object 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.

### Usage

    summarizeReplicates(object, summary ="min")

### Arguments

`object` | an object of class `cellHTS` that has already been normalized and scored (see details).
`summary` | 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).

### Details

A single value per probe is calculated by summarizing between scored replicates stored in the slot `assayData` of `object`. The summary is performed as follows:

- If `summary="mean"`, the average of replicate values is considered;

- If `summary="median"`, the median of replicate values is considered;

- If `summary="max"`, the maximum of replicate intensities is taken;

- If `summary="min"`, the minimum is considered, instead;

- If `summary="rms"`, the square root of the mean squared value of the replicates (root mean square) is taken as a summary function;

- If `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);

- If `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).

### Value

The `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 `state` to `object@state[["scored"]]= TRUE`.

### Author(s)

W. Huber huber@ebi.ac.uk, Ligia Bras ligia@ebi.ac.uk

### References

Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.

### See Also

`normalizePlates`, `summarizeChannels`, `scoreReplicates`, `imageScreen`.

### Examples

        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")

[Package cellHTS2 version 2.50.0 Index]