FOO, BAR, PLUGH, and WALDO expression

Description

This data set contains the expression levels of four imaginary proteins: FOO, BAR, PLUGH, and WALDO. Each sample on the RPPA slide is printed as a 5-step dilution series. There are 4x12 subgrids on each slide, corresponding to the 48 pins on the printer. Each subgrid contains 11 subrows and 11 subcolumns. Each subrow is composed of two 5-step dilution series from left to right, each series itself from most concentrated to most diluted, and a positive control spot. The eleventh subcolumn is composed of two mirrored 5-step positive control series, with most concentrated on top/bottom and most diluted near the middle; the middle is a negative control (typically blank).

When these slide images were quantified using MicroVigene, the whole slide was treated as a single subgrid (1x1x44x132) to save time (by not having to perform alignment on 48 individual subgrids).

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. The associated MicroVigene datafiles were converted back into their logical format (4x12x11x11) when read to facilitate downstream processing.

Format

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

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

  • Main.Row

  • Main.Col

  • Sub.Row

  • Sub.Col

  • SubgridAlias

  • SpotType

  • Dilution

  • GridAlias

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

  • Main.Row

  • Main.Col

  • Sub.Row

  • Sub.Col

  • SubgridAlias

  • SpotType

  • Dilution

  • GridAlias

  • Main.Row.Real

  • Main.Col.Real

  • Sub.Row.Real

  • Sub.Col.Real

Author(s)

P. Roebuck proebuck@mdanderson.org

Examples

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

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