Reads, Annotates, and Normalizes Reverse Phase Protein Array Data
Average biological replicates over different slides.
Calculates sample concentrations using linear model fit
Calculates sample concentrations using sigmoid model fit
Calculates the concentration of serial diluted samples
Corrects for background in an RPPA data set
Dilution series intersect correction
Sigmoidal curve prediction.
Data preprocessing
Estimates error model parameters var0 (basal variance) and varR (relat...
Logarithmize (log2) the first two RPPA list elements, i.e. foreground ...
Normalizes data in an RPPA data list
Select the highest concentration from serialy diluted samples
Scatter Plots from an RPPA data
Plot target and blank signal from RPPA control samples
qq-plot and qq-line of an RPPA data set
Draw time course from RPPA data
Multiplot function for RPPA time course datasets
Read and Annotate RPPA rawdata
Remove arrays from a RPPA data list
Draws boxplots of groups of an RPPA data set including wilcox or krusk...
Convert RPPA data into Expression Set
Draw a heatmap with column side colors from a RPPA data
Read, annotate and normalize reverse phase protein array data and get ...
GenePix result files
Aggregate the replicates in an RPPA data set
sample description file
sample description file
Selects the measurement samples from an RPPA data list
Selects samples from RPPA data
Draws boxplots of groups of an RPPA data set.
slide description file
slide description file
Tests for correlations in RPPA data
writes an RPPA data list into csv file
Reads in sample description and slide description files and annotates the expression values taken from GenePix results files (text file format used by many microarray scanner and software providers). After normalization data can be visualized as boxplot, heatmap or dotplot.