RPPanalyzer (version 1.3)

read.Data: Read and Annotate RPPA rawdata

Description

reads sampledescription and slidedescription txt files and annotates the median expression value in GenePix result files stored in current working directory.

Usage

read.Data(blocksperarray = 4, spotter = "arrayjet", writetable = FALSE,
   printFlags=FALSE,fileName="Flagged_spots.csv", remove_flagged=NULL, ...)

Arguments

blocksperarray

Integer describing the number of blocks in one array.

spotter

character strings: default arrayjet or aushon.

writetable

logical. If true data are exported as tab delimited text files to current working directory

printFlags

logical. If true flagged spots will exported as csv file

fileName

character string naming the csv file for the flagged spots

remove_flagged

Either NULL or an integer. If an integer, looks into column Flags of the gpr file and removes samples with flag value less than or equal -remove_flagged from the data tables.

...

any other arguments passed to read.gpr

Value

• expression
  matrix with protein expression data
• background
  matrix with background data
• arraydescription
  data frame with feature data
• sampledescription
  data frame with pheno data

Details

This function reads and annotates RPPA rawdata provided in three different kind of files. It is very important that these data files are in a correct format and stored in the same folder.

The file sampledescription.txt has to be a tab delimited text file with at least 6 columns named plate, column, row, sample_type, sample, concentration and in case of serially diluted samples a column dilution is required. The first 3 columns are describing the location of the sample in the source well plate. The 4th column describes the for different types of samples: measurement, control, neg_control or blank. In the column sample any character string describing the sample is possible. The column concentration has to contain only numerical values. Columns with further phenodata can be added. The slidedescription.txt describes the array properties. Required columns are: gpr (describing the name of the corresponding gpr file), the columns pad, slide, incubation_run, spotting_run containing integers are generating a unique array identifier. The column target describes the analyzed target and AB_ID the used antibody. Column with further feature data can be added. The third kind of files are the gpr files as results from image analysis software GenePix using the galfile from a aushon or arrayjet spotter.

Examples

library(RPPanalyzer)
  
  dataDir <- system.file("extdata", package="RPPanalyzer")
  setwd(dataDir)
  rawdata <- read.Data(blocksperarray=12, spotter="aushon", printFlags=FALSE, remove_flagged=NULL)
  print(dim(rawdata$expression))
  
  rawdata <- read.Data(blocksperarray=12, spotter="aushon", printFlags=FALSE, remove_flagged=50)
  print(dim(rawdata$expression))