scoreReplicates: Scores normalized replicate values given in a cellHTS object

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/summarizeReplicates.R

Description

This function scores the normalized replicate values stored in slot assayData of a cellHTS object. Current available options are to take the z-score value or the per-replicate normalized percent inhibition (NPI). Data are stored in slot assayData overridding its current content.

Usage

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scoreReplicates(object, sign="+", method="zscore", ...)

Arguments

object

an object of class cellHTS that has already been normalized.

sign

a character string, either "+" (default) or "-", which corresponds to multiplying the data by +1 or -1, respectively, after applying the scoring method specified by argument method. See details.

method

a character string indicating which method to use to score the replicate measurements. Available options are "none", "zscore" (default), "NPI". See details.

...

additional parameters required by some of the methods chosen in method.

Details

This function scores the normalized values given in the slot assayData of object. Current availabe scoring methods are:

After replicate scoring using the chosen method, the value given in sign ("+" or "-") is used to set the sign of the calculated scores. For example, with a sign="-", a strong decrease in the signal will be represented by a positive score, whereas setting sign="+", such a phenotype will be represented by a negative score. This option can be set to calculate the results to the commonly used convention.

Value

A cellHTS object with its slot assayData replaced with the scored values (same dimension).

Important: Note that the processing state "scored" of the cellHTS object is only updated to TRUE after summarizing the replicates, which is the next preprocessing step (see summarizeReplicates).

Author(s)

W. Huber huber@ebi.ac.uk, Ligia Braz 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, summarizeReplicates.

Examples

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    data(KcViabSmall)
    x <- normalizePlates(KcViabSmall, scale="multiplicative", method="median", varianceAdjust="none")
    x <- scoreReplicates(x, sign="-", method="zscore")
    x <- summarizeReplicates(x, summary="min") # conservative approach

cellHTS2 documentation built on May 31, 2017, 2:30 p.m.

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