Perform Robust Multi-array Average (RMA) procedure on Affymetrix microarray probe-level data
Expression = affyrma(CELFiles, CDFFile)
Expression = affyrma(ProbeStructure)
Expression = affyrma(CELFiles, CDFFile,
...'CELPath', CELPathValue, ...)
Expression = affyrma(CELFiles, CDFFile,
...'CDFPath', CDFPathValue, ...)
Expression = affyrma(...,
'Method', MethodValue, ...)
Expression = affyrma(...,
'Truncate', TruncateValue, ...)
Expression = affyrma(...,
'Median', MedianValue, ...)
Expression = affyrma(...,
'Output', OutputValue, ...)
Expression = affyrma(...,
'Showplot', ShowplotValue, ...)
Expression = affyrma(...,
'Verbose', VerboseValue, ...)
CELFiles | Any of the following:
|
CDFFile | Either of the following:
|
ProbeStructure | MATLAB® structure containing information from the
CEL files, including probe intensities, probe indices, and probe set
IDs, returned by the |
CELPathValue | Character vector or string specifying the path and folder where the files specified in
|
CDFPathValue | Character vector or string specifying the path and folder where the file specified in
|
MethodValue | Specifies the estimation method for the background adjustment model parameters. Choices
are |
TruncateValue | Specifies the background noise model. Choices are |
MedianValue | Specifies the use of the median of the ranked values
instead of the mean for normalization. Choices are |
OutputValue | Specifies the scale of the returned gene expression values. Choices are:
In the last instance, the data is transformed
as defined by the function |
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 For example:
|
VerboseValue | Controls the display of the status of the reading of
files and RMA processing. Choices are |
Expression | DataMatrix object containing the log2 based gene expression values that have been background adjusted, normalized, and summarized using the Robust Multi-array Average (RMA) procedure. Each
row in |
Expression = affyrma(CELFiles, CDFFile)Expression, a DataMatrix object containing
the log2 based gene expression values in a
matrix, the probe set IDs as row names, and the CEL file names as
column names. Note that each row in Expression corresponds
to a gene (probe set), 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.)
CELFiles is a character vector, string, string vector, or cell
array of character vectors containing CEL file names. CDFFile
is a character vector or string specifying a CDF file name. If you set
CELFiles to '*', then it reads all CEL
files in the current folder. If you set CELFiles to
' ', then it opens the Select CEL Files dialog box from which you
select the CEL files.
Note
For details on the reading of files and RMA processing, see celintensityread, rmabackadj, quantilenorm,
and rmasummary.
Expression = affyrma(ProbeStructure)ProbeStructure,
a MATLAB structure containing information from the CEL files,
including probe intensities, probe indices, and probe set IDs, returned
by the celintensityread function,
and returns Expression.
Expression = affyrma(...,
'PropertyName', PropertyValue,
...)affyrma 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:
specifies
a path and folder where the files specified by Expression = affyrma(CELFiles, CDFFile,
...'CELPath', CELPathValue, ...)CELFiles are
stored.
Expression = affyrma(CELFiles, CDFFile,
...'CDFPath', CDFPathValue, ...)CDFFile is
stored.
Expression = affyrma(...,
'Method', MethodValue, ...)MethodValue is 'RMA',
affyrma implements the estimation method described by Bolstad, 2005. When MethodValue is
'MLE', affyrma estimates the parameters using
maximum likelihood. Default is 'RMA'.
Expression = affyrma(...,
'Truncate', TruncateValue, ...)TruncateValue is false, affyrma uses
nontruncated Gaussian as the background noise model. Default is true.
Expression = affyrma(...,
'Median', MedianValue, ...)true or false (default).
Expression = affyrma(...,
'Output', OutputValue, ...)OutputValue can
be:
'log'
'log2'
'log10'
'linear'
@functionname
In the last instance, the data is transformed as defined by
the function functionname. Default is 'log2'.
Expression = affyrma(...,
'Showplot', ShowplotValue, ...)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.
(..., 'Showplot', [3,5,7],...) plots
the intensity values in columns 3, 5, and 7.
(..., 'Showplot', 3:9,...) plots
the intensity values in columns 3 to 9.
Expression = affyrma(...,
'Verbose', VerboseValue, ...)true (default) or false.
The following example assumes that you have the HG_U95Av2.CDF library
file stored at D:\Affymetrix\LibFiles\HGGenome,
and that your current folder points to a location containing CEL files
associated with this CDF library file. In this example, the affyrma function
reads all the CEL files in the current folder and a CDF file in a
specified folder. It also performs RMA background adjustment, quantile
normalization, and summarization procedures on the PM probe intensity
values, and returns a DataMatrix object, containing the metadata and
processed data.
Expression = affyrma('*', 'HG_U95Av2.CDF',...
'CDFPath', 'D:\Affymetrix\LibFiles\HGGenome');
[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] Mosteller, F., and Tukey, J. (1977). Data Analysis and Regression (Reading, Massachusetts: Addison-Wesley Publishing Company), pp. 165–202.
[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.
[4] Bolstad, B. (2005). “affy: Built-in Processing
Methods” https://www.bioconductor.org/packages/2.1/bioc/vignettes/affy/
inst/doc/builtinMethods.pdf
affygcrma | celintensityread | gcrma | mafdr | mattest | quantilenorm | rmabackadj | rmasummary