README.md

In steveneschrich/IncrementalRMA: Affymetrix-based RMA Processing Using Fixed Parameters

IncrementalRMA

Overview

IncrementalRMA works by applying previous computed parameters from a full RMA process. This function calculates the necessary parameters for future incrementalRMA use.

RMA consists of three steps: background correction, quantile normalization and median polish. Background correction is done per-chip, so there is no need for pre-calculating parameters. Quantile normalization computes values for each quantile in expression data and then sets the intensity distribution equal to these quantiles. Median polish sweeps out row-wise and column-wise medians from probe expression; column-wise effects are used as expression estimates.

Given the above description, quantiles (from quantile normalization) and row-wise effects (from median polish) can be computed on a set of samples and stored. With this information, incrementalRMA can then calculate gene expression from a new sample without re-computing these parameters.

This function computes these parameters and stores them in a list, such that the list can then be used. The elements of the list currently include:

• probeEffects: Row-wise effects from median polish step.
• normalizationVector: Quantile values from quantile normalization step.
• referenceCELFiles: An AffyBatch containing the reference cel files (for error calculations).}

A simple test of incrementalRMA is to parameterizeRMA, then apply incrementalRMA and compare with using rma on the set.

Installation

You can install the IncrementalRMA package from GitHub with:

# install.packages("devtools")
devtools::install_github("steveneschrich/IncrementalRMA")

Usage

There are two steps associated with IncrementalRMA: calculating the parameters (parameterizeRMA) and applying the parameters (incrementalRMA). As mentioned above, it is possible to verify that the software works by computing the parameters from an AffyBatch, applying the parameters to the same AffyBatch and comparing this to the canonical RMA approach.

BiocManager::install("affydata")
data(Dilution)
all.equal(exprs(incrementalRMA(Dilution, parameterizeRMA(Dilution))), exprs(affy::rma(Dilution)))

steveneschrich/IncrementalRMA documentation built on Dec. 23, 2021, 5:32 a.m.