The DS5RPPAPreFitQC class represents the inputs necessary to determine the quality control rating of a reverse-phase protein array slide with 5 dilution series.
# S4 method for DS5RPPAPreFitQC
qcprob(object, ...)
# S4 method for DS5RPPAPreFitQC
summary(object, ...)
object of class DS5RPPAPreFitQC
extra arguments for generic routines
Although objects of the class can be created by a direct call to
new, the preferred method is to use the RPPAPreFitQC
factory generator function.
antibody:character string specifying name of antibody
slopediff:numeric scalar specifying the difference from perfect slope
cvs:numeric vector containing the coefficient of variance for each positive control dilution series
slopes:numeric vector containing the slopes for each positive control dilution series
drdiffs:numeric vector containing the difference in dynamic range of each positive control dilution series
percentgood:numeric scalar specifying percentage of "good" sample spots on the slide
adjusted:logical scalar specifying if adjusted measures were used
Class RPPAPreFitQC, directly.
signature(object = "DS5RPPAPreFitQC"):
Calculates the probability of good slide, returned as numeric scalar.
signature(object = "DS5RPPAPreFitQC"):
Prints a summary of the underlying data frame.
P. Roebuck paul_roebuck@comcast.net, James M. Melott jmmelott@mdanderson.org
The prediction model used multiple training datasets from the RPPA Core Facility by fitting a logistic regression model using an expert rating of a slide's quality (good, fair, or poor) as the response variable and a host of metrics about the raw positive control data as predicting variables.
Ju Z, Liu W, Roebuck PL, Siwak DR, Zhang N, Lu Y, Davies MA,
Akbani R, Weinstein JN, Mills GB, Coombes KR
Development of a Robust Classifier for Quality Control of
Reverse Phase Protein Arrays.
Bioinformatics (2015) 31(6): 912-918.
https://pubmed.ncbi.nlm.nih.gov/25380958/