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Last data update: 2014.03.03
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R: Read PM or MM from CEL file into matrices
| read.celfile.probeintensity.matrices | R Documentation |
Read PM or MM from CEL file into matrices
Description
This function reads PM, MM or both types of intensities
into matrices. These matrices have all the probes for a probeset in
adjacent rows
Usage
read.celfile.probeintensity.matrices(filenames, cdfInfo, rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, verbose=FALSE, which= c("pm","mm","both"))
Arguments
filenames |
a character vector of filenames
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cdfInfo |
a list with items giving PM and MM locations for
desired probesets. In same structure as returned by make.cdf.package
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rm.mask |
a logical. Return these probes as NA if
there are in the [MASK] section of the CEL file
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rm.outliers |
a logical. Return these probes as NA if
there are in the [OUTLIERS] section of the CEL file
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.
rm.extra |
a logical. Return these probes as NA if
there are in the [OUTLIERS] section of the CEL file
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.
verbose |
a logical. When true the parsing routine
prints more information, typically useful for debugging.
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which |
a string specifing which probe type to return
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Value
returns a list of matrix items. One
matrix contains PM probe intensities, with probes in rows and arrays
in columns
Author(s)
B. M. Bolstad <bmb@bmbolstad.com>
Results
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providing 
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