affy-options {affy} | R Documentation

## Options for the affy package

### Description

Description of the options for the affy package.

### Note

The affy package options are contained in the Bioconductor options. The options are: begin{itemize}

- `use.widgets`: a logical used to decide on the default of widget use.
- `compress.cel`: a logical
- `compress.cdf`: a logical
- `probes.loc`: a list. Each element of the list is it self a list with two elements {it what} and {it where}. When looking for the informations about the locations of the probes on the array, the elements in the list will be looked at one after the other. The first one for which {it what} and {it where} lead to the matching locations information is used. The element {it what} can be one of {it package}, {it environment} or {it file}. The element {it where} depends on the corresponding element {it what}. begin{itemize}
- if {it package}: location for the package (like it would be for the argument `lib.loc` for the function `library`.
- if {it environment}: an `environment` to look for the information (like the argument `env` for the function `get`).
- if {it file}: a `character` with the path in which a CDF file can be found. end{itemize} end{itemize}

  ### Examples

      ## get the options
      opt <- getOption("BioC")
      affy.opt <- opt$affy

      ## list their names
      names(affy.opt)

      ## set the option compress.cel
      affy.opt$compress.cel <- TRUE
      options(BioC=opt)

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