read.probematrix {affy} | R Documentation

## Read CEL file data into PM or MM matrices

### Description

Read CEL data into matrices.

### Usage

    read.probematrix(..., filenames = character(0),
                     phenoData = new("AnnotatedDataFrame"),
                     description = NULL,
                     notes = "",
                     compress = getOption("BioC")$affy$compress.cel,
                     rm.mask = FALSE, rm.outliers = FALSE, rm.extra = FALSE,
                     verbose = FALSE, which = "pm", cdfname = NULL)

### Arguments

`...` | file names separated by comma.
`filenames` | file names in a character vector.
`phenoData` | a `AnnotatedDataFrame` object.
`description` | a `MIAME` object.
`notes` | notes.
`compress` | are the CEL files compressed?
`rm.mask` | should the spots marked as 'MASKS' set to `NA`?
`rm.outliers` | should the spots marked as 'OUTLIERS' set to `NA`?
`rm.extra` | if `TRUE`, overrides what is in `rm.mask` and `rm.oultiers`.
`verbose` | verbosity flag.
`which` | should be either "pm", "mm" or "both".
`cdfname` | Used to specify the name of an alternative cdf package. If set to `NULL`, the usual cdf package based on Affymetrix's mappings will be used.

### Value

A list of one or two matrices. Each matrix is either PM or MM data. No `AffyBatch` is created.

### Author(s)

Ben Bolstad bmb@bmbolstad.com

### See Also

`AffyBatch`, `read.affybatch`

[Package affy version 1.64.0 Index]