##################################################
# An R Software Tool for Protein Microarray Data Analysis
# -1.use to read/import the data
# -2.background correct the raw data
# -3.apply the gainscan power funciton model to integrate the array data acquired under different PMT settings
# -3.normalize between arrays, by a linear model on log-transformed data
# ToDo:
# -4.statistically identify the differentially interacting protein features between samples
# with correction for multiple comparison
#
# developed by Feng Feng @ Boston University.
# All right reserved
# 10/27/2017
####################################################
##the following is the code to install necessary libs manually
## try http:// if https:// URLs are not supported
#source("https://bioconductor.org/biocLite.R")
#biocLite("limma")
#####################
##########Dependency###########
## library(limma)
####################
#' @include fileIO.R
# # ' @include data.R
#'
#' @title gainscan to preprocess and analyze protoarray data
#'
#' @description An R package to read, preprocess and analyze protoarray data
#'
#' @details The functions you are likely to need from \pkg{gainscan} are
#' to read and normalize arrays. Most importantly we can process array data
#' acquired multiple times under different PMT voltages. The data from multiple
#' scans will be fitted for a power function with a baseline and then the incident
#' light signal from each spot will be estimated. This way, the data quality is
#' improved and the technical variations are significantly reduced.\cr
#' Please refer to the vignettes to see the explanations and examples.
#'
#'\cr
#'-------------\cr
#'Currently the package can do the followings \cr
#' \enumerate{
#' \item use to read/import the data
#' \item background correct the raw data
#' \item apply the gainscan power funciton model to integrate the array data acquired under different PMT settings
#' \item normalize between arrays, by a linear model on log-transformed data \cr\cr
#'ToDo:
#' \item run differential analysis to statistically identify the positive interacting protein features
#' with correction for multiple comparison
#' \item add a section to describe in vignettes about the differential analysis and FDR.
#' }
#'\cr
#'
"_PACKAGE"
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