chipArrayStatistics: Statistics of beadLevelData

In blima: Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level

Description

This function returns table with statistics of single beadLevelData object indexed by order of spots. It prints number of beads on each array spot mean foreground intensity and optionally mean background intensity, mean number of beads in probe set and unbiased estimate of standard deviations of these parameters. Optionaly you can also obtain percentage of removed beads within excludedOnSDMultiple multiple of standard deviations from the background value.

Usage

chipArrayStatistics(b, includeBeadStatistic = TRUE, channelForeground = "GrnF", 
    channelBackground = "GrnB", includeBackground = TRUE, excludedOnSDMultiple = NA)

Arguments

b	Single beadLevelData object.
includeBeadStatistic	Include number of beads per probe in output.
channelForeground	Name of channel of foreground.
channelBackground	Name of channel of background.
includeBackground	Whether to output background data.
excludedOnSDMultiple	If positive number, print how much percents of the background lies more than excludedOnSDMultiple multipliers of standard deviation estimate away from background mean.

Author(s)

Vojt<c4><9b>ch Kulvait

Examples

if(require("blimaTestingData") && interactive())
{
    #To print basic statistic data about blimatesting[[1]] object.
    data(blimatesting)
    array1stats = chipArrayStatistics(blimatesting[[1]], includeBeadStatistic=TRUE,
            excludedOnSDMultiple=3)
    array1pheno = pData(blimatesting[[1]]@experimentData$phenoData)
    array1stats = data.frame(array1pheno$Name, array1stats)
    colnames(array1stats)[1] <- "Array";
    print(array1stats);
}else
{
    print("To run this example, please install blimaTestingData package from bioconductor by running BiocManager::install('blimaTestingData').");
}

blima documentation built on Nov. 8, 2020, 8:15 p.m.