This function scores the normalized replicate values stored in slot
assayData of a
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.
an object of class
a character string, either "+" (default) or "-", which corresponds to multiplying the data by
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
This function scores the normalized values given in the slot
Current availabe scoring methods are:
method="none", no scoring is applied.
method="zscore" (robust z-scores), for each replicate, this is calculated by subtracting the overall median from each measurement and dividing the result by the overall
mad. These are estimated for each replicate by considering the distribution of intensities (over all plates) in the wells whose content is annotated as
method="NPI" (normalized percent inhibition applied in a per-replicate basis, i.e. using the overall mean of positive and negative controls across all plates of a given replicate), for each replicate, this method consists of subtracting each measurement from the average of the intensities on the positive controls (taken across all plates), and this result is then divided by the difference between the averages of the measurements on the positive and the negative controls (taken across all plates). If this method is chosen, one may need to provide further arguments to
scoreReplicates, namely, arguments
negControls. These arguments should be vectors of regular expression patterns specifying the name of the positive(s) and negative(s) controls, respectivey, as provided in the plate configuration file. The length of these vectors should match the current number of channels in
dim(Data(object))). By default, if
negControls are not given, pos and neg will be taken as the name for the wells containing positive or negative controls. The content of
negControls is passed to
regexpr for pattern matching within the well annotation given in the
featureData slot of
object (which can be accessed via
wellAnno(object)) (see examples for
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.
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
after summarizing the replicates, which is the next preprocessing step (see
Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.
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