simpleaffy (version 2.48.0)

read.affy.mixed: Read a Set of .CEL Files and Phenotypic Data from mixed chip types

Description

Reads the specified file, which defines phenotypic data for a set of .CEL files. Reads the specified files into an AffyBatch object and then creates a phenoData object, defining the experimental factors for those chips. This function deals with different array types by generating a pseudo arrayset containing only the probes in common. It does this by finding the smallest chip type in the set, and using this as a template. Probesets that aren't shared are set to 0. Other probesets are copied in. Note that this means that spots that were in one place on one array, appear to be at a different place on another. What this does to position specific background correction algorithms (such as mas5) is left as an exercise to the reader). Beware...

Usage

read.affy.mixed(covdesc = "covdesc",path=".", ...)

Arguments

covdesc

A white space delimited file suitable for reading as a data.frame. The first column (with no column name) contains the names(or paths to) the .CEL files to read. Remaining columns (with names) represent experimental factors for each chip. these become elements of the phenoData object.

...

extra functions to pass on to ReadAffy

path

The path to prefix the filenames with before calling ReadAffy

Value

An AffyBatch object

References

http://bioinformatics.picr.man.ac.uk/

See Also

ReadAffy, AffyBatch data.frame phenoData

Examples

  ## Not run: 
#     eset <- read.affy.mixed(); # read a set of CEL files
#   
#     eset.rma <- call.exprs(eset,"rma");   
#   ## End(Not run)