BackgroundCutoff: Visualize arrays to identify cutoff for background...

In TomNash/NASHMAP: Microarray Analysis Pipeline

Description

Plot the histogram of max gene illumination across all arrays to identify cutoff for background subtraction. Upper and lower limits can be changed to narrow focus. Plots will be saved in analysis pipeline directory.

Usage

BackgroundCutoff(preprocess.data.obj, method=c("mloess","quantile",
"raw"), xlim.lo=0, xlim.hi)

Arguments

preprocess.data.obj	Object returned from call to preprocess.data
method	Type of normalization to use: "quantile" for quantile normalization; "mloess" for MLOESS normalization; "raw" for raw data
xlim.lo	Lower bound on X for histogram plot (binary logarithm)
xlim.hi	Upper bound on X for histogram plot (binary logarithm)

TomNash/NASHMAP documentation built on May 9, 2019, 4:54 p.m.