rppaTriple-extdata: ACTB, CAS3, FAK, and ODC1 expression in 14 fed/starved cell...

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This data set contains the expression levels of four proteins: beta-Actin (ACTB), Caspase 3 (CAS3), Focal adhesion kinase (FAK), and Ornithine decarboxylase (ODC1) from a study that was done to compare protein levels in 14 cell lines from both a “fed” and a “starved” state. There are two files included for beta-Actin, one that was scanned in color (actb) and the other in 16-bit grayscale (actb.gray); all other proteins were scanned in color.

This data set also contains a description of the design used for the reverse-phase protein arrays from this study. Cell lysates were spotted on the array in six-step dilution series. The layout of the array consists of a grid of 6x6 subgrids. The first three rows of a subgrid contain 3 replicates of a cell line. The last three rows contain 3 replicates of another cell line. Each subgrid is replicated on the array 3 times, so that there are a total of 9 replicates per cell line per state. The top part of the array contains the fed cell lines and the bottom part of the array contains the starved cell lines. There is one subgrid on the array that contains only buffer material and another subgrid that did not have anything printed (blank). There are a total of 18 spots each of buffer and blank material.


The MicroVigene TXT datafiles contain the following columns:

  • Main Row

  • Main Col

  • Sub Row

  • Sub Col

  • GeneID

  • mean_net

  • mean_total

  • mean_bkg

  • bkg_used

  • mean_dust

  • median_net

  • median_total

  • median_bkg

  • vol_net

  • vol_total

  • vol_bkg

  • vol_dust

  • cv_spot

  • cv_bkg

  • xcenter

  • ycenter

  • area_signal

  • area_spot

  • area_bkg

  • solidity

  • circularity

  • roundness

  • aspect

  • dustiness

  • rank

  • type

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

  • Antibody

  • Filename

  • Alias

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

  • Alias

  • Sample


P. Roebuck proebuck@mdanderson.org


Victor Levin


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

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

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