UPC_Generic_ExpressionSet: Generic function to apply Universal exPression Codes (UPC) transformation to ExpressionSet objects

Description

This function can be used to derive UPC values for any type of gene-expression data. The key prerequisite is that the data be placed into an ExpressionSet object. And optionally, the user can specify the length and/or GC content (proportion of G or C bases) for the corresponding genomic region (e.g., gene). If these values are specified, the UPC algorithm will correct for biases resulting from length or GC content.

Usage

UPC_Generic_ExpressionSet(expressionSet, sequenceFeatureName = NA, modelType = "nn", convThreshold = 0.001, higherValuesIndicateHigherExpression = TRUE, verbose = TRUE)

Arguments

expressionSet

An ExpressionSet object that contains data to be UPC transformed. Required.

sequenceFeatureName

Optionally, the DNA sequence corresponding to each feature (e.g., microarray probe) can be specified in the ExpressionSet object's metadata. If specified, the UPC transformation will take the G/C content and length of each feature into account. Optional.

modelType

Various models can be used for the mixture model to differentiate between active and inactive probes. The default is the normal-normal model (``nn''), which uses the normal distribution. Other available options are log-normal (``ln''), negative-binomial (``nb''), and normal-normal Bayes (``nn_bayes'').

convThreshold

Convergence threshold that determines at what point the mixture-model parameters have stabilized. The default value should be suitable in most cases. However, if the model fails to converge (or converges too quickly), it may be useful to adjust this value. (This parameter is optional.)

higherValuesIndicateHigherExpression

In most cases, higher expression values indicate relatively high expression. However, if higher values indicate relatively low expresssion, this parameter can be used to indicate such. Accordingly, UPC values closer to one will indicate higher expression, and UPC values closer to zero will indicate the opposite. (This parameter is optional.)

verbose

Whether to output more detailed status information as processing occurs. Default is TRUE.

Value

An ExpressionSet object with UPC values.

References

Piccolo SR, Withers MR, Francis OE, Bild AH and Johnson WE. Multi-platform single-sample estimates of transcriptional activation. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110:44 17778-17783.

Examples

Run this code

## Not run: 
# upcData = UPC_Generic_ExpressionSet(getGEO("GSE56234", GSEMatrix=TRUE)[[1]], sequenceFeatureName="SEQUENCE")
# ## End(Not run)

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