BatchAdjust


    An <code>ExpressionSet</code> object that contains data to be adjusted for batch effects. This object should contain at least one <code>phenoData</code> column that indicates the batch number for each sample. Covariates may also be specified in other <code>phenoData</code> columns. Required.


expressionSet


    Name of <code>phenoData</code> column that indicates the batch number for each sample. Required.


batchVariableName


    Name(s) of <code>phenoData</code> column(s) that indicate the covariate information for each sample. Optional.


covariateVariableNames


  This is a convenience function for adjusting an ExpressionSet object for batch effects.


SCAN is a microarray normalization method to facilitate
personalized-medicine workflows. Rather than processing
microarray samples as groups, which can introduce biases and
present logistical challenges, SCAN normalizes each sample
individually by modeling and removing probe- and array-specific
background noise using only data from within each array. SCAN
can be applied to one-channel (e.g., Affymetrix) or two-channel
(e.g., Agilent) microarrays. The Universal exPression Codes
(UPC) method is an extension of SCAN that estimates whether a
given gene/transcript is active above background levels in a
given sample. The UPC method can be applied to one-channel or
two-channel microarrays as well as to RNA-Seq read counts.
Because UPC values are represented on the same scale and have
an identical interpretation for each platform, they can be used
for cross-platform data integration.

Stephen R Piccolo

SCAN.UPC

Single-channel array normalization (SCAN) and Universal
exPression Codes (UPC)

BatchAdjust function

An <code>ExpressionSet</code> object that contains data to be adjusted for batch effects. This object should contain at least one <code>phenoData</code> column that indicates the batch number for each sample. Covariates may also be specified in other <code>phenoData</code> columns. Required.

Name of <code>phenoData</code> column that indicates the batch number for each sample. Required.

Name(s) of <code>phenoData</code> column(s) that indicate the covariate information for each sample. Optional.

This is a convenience function for adjusting an ExpressionSet object for batch effects.

BatchAdjust: Helper function for applying the ComBat batch-adjusting methodology to an ExpressionSet object

Description

Usage

Arguments

Value