rppaTumor-extdata: ERK2, GSK3, and JNK expression in tumor samples

In SuperCurveSampleData: SuperCurve RPPA Sample Data

Description

This data set contains the expression levels of three proteins: ERK2, GSK3, and JNK in 96 breast tumor samples and controls, measured in dilution series using reverse-phase protein arrays.

This 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. Cell lysates were spotted on the array in seven-step dilution series with eith a positive or negative control at the end of the series. The layout of the array consisted of a grid of 4x4 subgrids. The first two rows of a subgrid contained a single dilution series and a negative control spot. The last two rows of the subgrid contained another dilution series and a positive control spot.

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_net

• vol_bkg

• vol_dust

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

• Antibody

• Filename

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

• Alias

• Sample

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

• Main.Row

• Main.Col

• Sub.Row

• Sub.Col

• SubgridAlias

• SpotType

• Dilution

The file ‘supercurve.csv’ contains the following columns:

• CA19-9

• ERK2

• GSK3

• JNK

• p38

Author(s)

P. Roebuck [e-mail]

Source

Doris Swank and Gordon Mills

Examples

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

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

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