affyPreprocess.affy: Preprocess using affy package
In ShixiangWang/iProfile: integrated cancer Profile using multiple datasets

Description Usage Arguments Details Value Author(s) See Also

Preprocess affymetrix cel files using affy package

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affyPreprocess.affy(data.dir = getwd(), Isgzipped = TRUE,
  useFullNames = TRUE, modifyNames = TRUE, method = c("RMA", "gcRMA"),
  ...)

`data.dir`	a character. Set the directory path of raw data, use work directory as default.
`Isgzipped`	a logical value. Specify if the cel files are gzipped, use TRUE as default.
`useFullNames`	a logical value. If TRUE, the directory path is prepended to the file names to give a relative file path. If FALSE, the file names (rather than paths) are returned.
`modifyNames`	a logical value. Raw data download from NCBI GEO database are named as "GSMXXXXX.CEL.gz" if gzipped or "GSMXXXXX.CEL" if unzipped. If TRUE, ".CEL.gz" or ".CEL" will be chopped off.
`method`	a character. "RMA" or "gcRMA" can be used.

Affy package is a very useful bioconductor package used to preprocess chips produced by Affymetrix and use files provided by the manufacturers in their native format. Here we use it load raw data files and preprocess expressing data by implementing the RMA, gcRMA algorithm and so on.

an ExpressionSet Object

Shixiang Wang <w_shixiang@163.com>

ExpressionSet,rma, rma, gcrma, affyPreprocess.oligo