INCATomeData {INCATome}

Translatome microarray dataset simulated from experimentally acquired translatome of Hela cells.

Description

An RGList object for raw translatome data (based on one array and its dyesawapped array) simulated to produce n=12 arrays (n[CTRL]=3, n[CDT]=3, n[CTRLdyeswapped]=3, n[CDTdyeswapped]=3). Simulation was performed so that 25% of genes are deregulated and that this deregulation is skewed by 70% towards downregulation.

Usage

data("INCATomeData")

Format

The data contain a list of 6 objects: 4 RGLists and two dataframes.

RGdata

an RGList object containing R, G, Rb, Gb, targets and source. The main data dimensions are ncol=12 arrays and nrow=2000 probes. The geneset can be fragmented as follows: from 1 to 1664: general probes, from 1665 to 1677: ACTB probes, from 1678 to 1680: PABPC1 probes and from 1681 to 2000: SpikeIn probes

RGdataBG

an RGList object of background corrected data containing R, G, targets and source

RGdataNM

an RGList object of INCA normalised data containing R, G, targets and source

RGdataDS

an RGList object of dyeswapped data containing R, G, targets and source

idata

a dataframe containing the Internal Reference (ACTB and PABPC1) Expected logged Ratios for each array as determined experimentally.

sdata

a dataframe containing the SpikeIn Expected Ratios for each probe as defined experimentally by the manufacturer.

Source

Sbarrato T., Spriggs R.V., Wilson L., Jones C., Dudek K., Bastide A., Pichon X., Poyry T. and Willis A.E., RNA, 2017 Aug 25, An Improved Analysis Methodology for Translational Profiling by Microarray, DOI:10.1261/rna.060525.116

Examples

data(INCATomeData)