rppaCell-extdata: AKT, ERK2, and CTNNB1 expression in cell lines

In SuperCurveSampleData: SuperCurve RPPA Sample Data

Description

This data set contains the expression levels of three proteins: AKT, ERK2, and beta catenin (CTNNB1) in 40 cell lines, measured in duplicate dilution series using reverse-phase protein arrays.

The data set also contains a description of the design of the reverse-phase protein array used in a set of experiments to measure protein levels in 40 different cell lines. Cell lysates were spotted on the array in duplicate in eight-step dilution series. The layout of the array consisted of a grid of 4x4 subgrids. Each subgrid contained the duplicate dilution series for a single sample. Each of the identical top two rows of a subgrid contained the four most concentrated dilution steps (in decreasing concentrations from left to right), and the identical bottom two rows contained the four least concentrated dilution steps.

Format

The MicroVigene TXT datafiles contain the following columns:

• Main Row

• Main Col

• Sub Row

• Sub Col

• GeneID

• mean_net

• mean_total

• median_net

• vol_bkg

• vol_dust

The file ‘proteinAssay.tsv’ contains the following columns:

• Antibody

• Filename

The file ‘cellLineInfo.tsv’ contains the following columns:

• CellLine

• ProteinConcentration

• LoadingControl

Author(s)

P. Roebuck [e-mail]

Source

Bryan Hennessey and Gordon Mills

Examples

## Path to raw data directory
extdata.dir <- system.file("extdata", package="SuperCurveSampleData")
rawdata.dir <- file.path(extdata.dir, "rppaCellData")
rawdata.dir

## Directory Listing
files <- list.files(rawdata.dir, full.names=TRUE)
files

SuperCurveSampleData documentation built on May 2, 2019, 6:08 p.m.