beadtypeFilter: Filter Illumina bead arrays

Description Usage Arguments Details Value Author(s) References Examples

View source: R/beadtypeFilter.R

Description

This is a wrapper function for the iccFun function and it implements the filtering method of Forcheh et al. (2012). It takes a normalized ExpressionSetIllumina object,a LumiBatch object or a normalized data.frame and returns the names of the informative bead types. Optionally, the filtered ExpressionSetIllumina object or the filtered data.frame can also be returned.

Usage

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beadtypeFilter(beadsum, Quantile = 1, keepData = TRUE, delta = 0.5)

Arguments

beadsum

A normalized data object, which can be an ExpressionSetIllumina, LumiBatch or a normalized data.frame.

Quantile

It refers to the number summary described in Forcheh et al. (2012). It is the quantile at which summarization of the ICC is done. For example, iccQuant = 0 means that summarization of the ICCs be done at the minimum ICC, 0.75 means summarization be done at the 75 quantile. Note that filtering will also be done at this specified quantile. For example, iccQuant = 1 means that the ICCs be summarized only using the maximum ICC and that beads be filtered using the maximum ICC.

keepData

If TRUE, then, the filtered object (i.e., filtered ExpressionSetIllumina object or filtered data.frame) and the identification names of the informative bead types are returned. If FALSE, only the identification names of the informative bead types will be returned.

delta

The proposed cutoff point at which a bead type should be declared informative or non-informative. The default is 0.5.

Details

Bead filtering aims at removing non-informative bead types prior to the downstream analysis.

This function is a wrapper of the iccFun function and it performs bead filtering. It takes a normalized ExpressionSetIllumina object or a normalized data.frame as input and so, the user should do the appropriate data normalization prior to submitting the ExpressionSetIllumina object or data.frame to the function. Refer to the “beadarray" package documentation for more on how to obtain a normalized ExpressionSetIllumina object. If a data.frame is used, make sure that the column names are similarly to the ones from BeadStudio: column names for bead averages should end with "Signal", standard errors should end with "STDERR" and number of beads used for the data sumarization should end with "NBEADS".

Value

InformProbeNames

Names of the Informative bead types

informData

The filtered ExpressionSetIllumina object or filtered data.frame

Author(s)

Anyiawung Chiara Forcheh, Geert Verbeke, Adetayo Kasim, Dan Lin, Ziv Shkedy, Willem Talloen, Hinrich WH Gohlmann, Lieven Clement.

References

Dunning, M.J., Smith, M.L., Ritchie, M.E., Tavare, S. (2007). beadarray: R classes and methods for Illumina bead-based data, Bioinformatics. 23(16):2183-2184.

Dunning, M.J. (2011). beadarrayExampleData: Example data for the beadarray package. R package version 1.0.4.

Forcheh, A.C, Verbeke, G., Kasim, A., Lin, D., Shkedy, Z., Talloen, W., Gohlmann, H.W.H, Clement, L. (2012). Gene Filtering in the Analysis of Illumina Microarray Experiments, Statistical Applications in Genetics and Molecular Biology, Berkeley Electronic Press, vol. 11(2), Article 3.

Kim, R.S. and Lin, J. (2011). Multi-level mixed effects models for bead arrays. Bioinformatics, 27(5):633-640.

Examples

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require(beadarrayExampleData)
data(exampleSummaryData)
exampleSummaryDataNorm <- normaliseIllumina(channel(exampleSummaryData, "G"),
method = "quantile", transform = "none")
iccResults<-beadtypeFilter(exampleSummaryDataNorm[1:100,],Quantile=1,keepData=FALSE,delta=0.5)

beadarrayFilter documentation built on May 29, 2017, 7:09 p.m.