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rmabackadj

Perform background adjustment on Affymetrix microarray probe-level data using Robust Multi-array Average (RMA) procedure

Syntax

BackAdjustedMatrix = rmabackadj(PMData)
BackAdjustedMatrix = rmabackadj(..., 'Method', MethodValue, ...)
BackAdjustedMatrix = rmabackadj(..., 'Truncate', TruncateValue, ...)
BackAdjustedMatrix = rmabackadj(..., 'Showplot', ShowplotValue, ...)

Input Arguments

PMData

Matrix of intensity values where each row corresponds to a perfect match (PM) probe and each column corresponds to an Affymetrix® CEL file. (Each CEL file is generated from a separate chip. All chips should be of the same type.)

MethodValue

Specifies the estimation method for the background adjustment model parameters. Enter either 'RMA' (to use estimation method described by Bolstad, 2005) or 'MLE' (to estimate the parameters using maximum likelihood). Default is 'RMA'.

TruncateValue

Specifies the background noise model. Enter either true (use a truncated Gaussian distribution) or false (use a nontruncated Gaussian distribution). Default is true.

ShowplotValue

Controls the plotting of a histogram showing the distribution of PM probe intensity values (blue) and the convoluted probability distribution function (red), with estimated parameters mu, sigma and alpha. Enter either 'all' (plot a histogram for each column or chip) or specify a subset of columns (chips) by entering the column number, list of numbers, or range of numbers.

Output Arguments

BackAdjustedMatrixMatrix of background-adjusted probe intensity values.

Description

BackAdjustedMatrix = rmabackadj(PMData) returns the background adjusted values of probe intensity values in the matrix, PMData. Note that each row in PMData corresponds to a perfect match (PM) probe and each column in PMData corresponds to an Affymetrix CEL file. (Each CEL file is generated from a separate chip. All chips should be of the same type.) Details on the background adjustment are described by Bolstad, 2005.

BackAdjustedMatrix = rmabackadj(..., 'PropertyName', PropertyValue, ...) calls rmabackadj with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

BackAdjustedMatrix = rmabackadj(..., 'Method', MethodValue, ...) specifies the estimation method for the background adjustment model parameters. When MethodValue is 'RMA', rmabackadj implements the estimation method described by Bolstad, 2005. When MethodValue is 'MLE', rmabackadj estimates the parameters using maximum likelihood. Default is 'RMA'.

BackAdjustedMatrix = rmabackadj(..., 'Truncate', TruncateValue, ...) specifies the background noise model used. When TruncateValue is false, rmabackadj uses nontruncated Gaussian as the background noise model. Default is true.

BackAdjustedMatrix = rmabackadj(..., 'Showplot', ShowplotValue, ...) lets you plot a histogram showing the distribution of PM probe intensity values (blue) and the convoluted probability distribution function (red), with estimated parameters mu, sigma and alpha. When ShowplotValue is 'all', rmabackadj plots a histogram for each column or chip. When ShowplotValue is a number, list of numbers, or range of numbers, rmabackadj plots a histogram for the indicated column number (chip).

For example:

  • (..., 'Showplot', 3,...) plots the intensity values in column 3 of PMData.

  • (..., 'Showplot', [3,5,7],...) plots the intensity values in columns 3, 5, and 7 of PMData.

  • (..., 'Showplot', 3:9,...) plots the intensity values in columns 3 to 9 of PMData.

Examples

  1. Load a MAT-file, included with the Bioinformatics Toolbox™ software, which contains Affymetrix probe-level data, including pmMatrix, a matrix of PM probe intensity values from multiple CEL files.

    load prostatecancerrawdata
  2. Perform background adjustment on the PM probe intensity values in the matrix, pmMatrix, creating a new matrix, BackgroundAdjustedMatrix.

     BackgroundAdjustedMatrix = rmabackadj(pmMatrix);
  3. Perform background adjustment on the PM probe intensity values in only column 3 of the matrix, pmMatrix, creating a new matrix, BackgroundAdjustedChip3.

     BackgroundAdjustedChip3 = rmabackadj(pmMatrix(:,3));

The prostatecancerrawdata.mat file used in the previous example contains data from Best et al., 2005.

References

[1] Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U., Speed, T.P. (2003). Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Biostatistics 4, 249–264.

[2] Bolstad, B. (2005). “affy: Built-in Processing Methods” http://www.bioconductor.org/packages/2.1/bioc/vignettes/affy/ inst/doc/builtinMethods.pdf

[3] Best, C.J.M., Gillespie, J.W., Yi, Y., Chandramouli, G.V.R., Perlmutter, M.A., Gathright, Y., Erickson, H.S., Georgevich, L., Tangrea, M.A., Duray, P.H., Gonzalez, S., Velasco, A., Linehan, W.M., Matusik, R.J., Price, D.K., Figg, W.D., Emmert-Buck, M.R., and Chuaqui, R.F. (2005). Molecular alterations in primary prostate cancer after androgen ablation therapy. Clinical Cancer Research 11, 6823–6834.

Introduced in R2006a

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