Usage
createAB(object, verbose=TRUE, ref.channel="R", genes.block=NULL, genes.row=NULL, genes.col=NULL, genes.id=NULL, genes.name=NULL, galname=NULL, env.overwrite=TRUE, ...)
Arguments
object
An appropriate EListRaw, RGList, MAList or list object.
verbose
Logical. The default value is TRUE. The details of the function execution are displayed on the console.
genes.block
Optional character vector in case the platform is neither ImaGene, Exiqon nor Agilent. The name of the column
in the object$genes data frame that contains the block or field values.
genes.row
Optional character vector in case the platform is neither ImaGene, Exiqon nor Agilent. The name of the column
in the object$genes data frame that contains the row values.
genes.col
Optional character vector in case the platform is neither ImaGene, Exiqon nor Agilent. The name of the column
in the object$genes data frame that contains the column values.
genes.id
Optional character vector in case the platform is neither ImaGene, Exiqon nor Agilent. The name of the column
in the object$genes data frame that contains the gene IDs.
genes.name
Optional character vector in case the platform is neither ImaGene, Exiqon nor Agilent. The name of the column
in the object$genes data frame that contains gene names.
ref.channel
Character vector. The value of the reference channel for two-color arrays ('R' or 'G')
galname
Character vector. The default value is NULL. In this case the GAL annotation
environment used by createAB for generating the resulting AffyBatch
object is lost. Assigning galname a non-empty value allows to control this GAL
environment, which is useful in two specific situations. First, it gives a handle to this
GAL annotation environment for later use. Second, if an adequate GAL annotation environment already
exists in the memory (e.g. after having been generated by createAB or by
make.gal.env), galname allows to force createAB to use it for
generating the resulting AffyBatch object.
env.overwrite
Logical. The default value is TRUE. If a GAL annotation environment with the
same name already exists in the memory, it will be overwritten. This may be useful
when the piece of code containing createAB is run several times.
...
Any additional argument that can be given to the AffyBatch constructor, as specified
in the documentation of the AffyBatch object provided in the affy package.