INCATome (version 1.0)

INCA.DEG: INCATome Deregulated Genes Identification

Description

Performs the INCATome DEG identification for microarray data, consisting of an overlap of at least two out of four DEG tests (TTest, Limma, RankProd and SAM).

Usage

INCA.DEG(x, cl, wcol, filt = TRUE, selneg, base = 2, highlight = NULL)

Arguments

x

an RGList object

cl

a vector specifying type of samples, 0 being control and 1 being condition.

wcol

an integer specifying the number of the column where Gene Names can be found in the gene annotation table.

filt

logical, TRUE if a set of negative control probes are to be used for filtering. Filtering is performed by removing any probes for which the average intensities are lower than the "negative" mean +/- 1.5 "negative" deviation.

selneg

a character or vector containing the negative control probe names for filtering.

base

an integer specifying the log base. Default is 2.

highlight

a character vector specifying a set of genes of interest. These will be highlighted in the graphical representations.

Value

A List object containing the INCA DEG output for significant DEGs with INCA DEG Score >= 2, as well as all individual outputs from the different tests. Additionally, volcanoplots for each test will be generated.

Examples

# NOT RUN {
#Load the INCATome Dataset
data(INCATomeData)
attach(INCATomeData)
out=INCA.DEG(RGdataDS,c(0,0,0,1,1,1),8,filt=TRUE,
 selneg="NegativeControl", highlight=c("ACTB","PABPC1"))
# }