DetectionCalls-methods: DetectionCalls

In drmjc/microarrays: A collection of microarray and genomic helper code.

Description

From microarray data, extract the detection p-values, and convert to P/M/A calls, ie Present/Marginal/Absent.

Arguments

x	an ExpressionSet, or LumiBatch object
thresh	a numeric(2) where the values represent the p-value thresholds for Present and Marginal, respectively. Some guidance re Illumina detection pvals here http://www.illumina.com/Documents/products/technotes/technote_gene_expression_data_quality_control.pdf

Value

a character matrix, same dimension as x

Affymetrix Genome/IVT arrays

Older generation Affymerix arrays use affy::mas5calls, where the thresholds are c(0.04, 0.06).

Affymetrix ST arrays

ST arrays, that use the DABG procedure for detection pvalues need to have quite stringent p-value thresholds. We recommend c(1e-05, 0.001).

LumiBatch objects

As far as I can tell, BeadStudio and GenomeStudio differ in how they report detection p-values. BeadStudio (older) has low values indicating expression; GenomeStudio reports 1-p, thus high values indicate high expression. This is true at least for BeadStudio 1.4.0.1, and GenomeStudio 1.8.0 files. In either case, the values for thresh should be small (default=c(0.01, 0.05)), and for GenomeStudio, the logic will be reversed such that probes with p-val > 0.95 are Marginal, and p-val > 0.99 are Present.

Author(s)

Mark Cowley

Examples

require(lumi)
data(example.lumi)
head(DetectionCalls(example.lumi))

drmjc/microarrays documentation built on May 15, 2019, 2:26 p.m.