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

Description Usage Arguments Details Value Author(s) See Also

Preprocess affymetrix cel files using oligo package, parallel computing is supported

1 2	affyPreprocess.oligo(data.dir = getwd(), Ncores = 1, useMaxCores = TRUE, Isgzipped = TRUE, useFullNames = TRUE, modifyNames = TRUE)

`data.dir`	a character. Set the directory path of raw data, use work directory as default.
`Ncores`	a integer number. Set how many CPU cores you want to use for computation.
`useMaxCores`	a logical value. Specify if all CPU cores used for computing, use TRUE as default. if the value is TRUE, it will overwrite the Ncores parameter and find how many cores your machine have and register the number for use. If you don't want this, please set the value to FALSE and set the Ncores.
`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.

Oligo package is a very useful and common bioconductor package used to preprocess chips produced by Affymetrix and NimbleGen and use files provided by these manufacturers in their native format. Here we use it load raw data files and preprocess expressing data by implementing the RMA algorithm.

an ExpressionSet Object

Shixiang Wang <w_shixiang@163.com>

ExpressionSet, rma

ShixiangWang/iProfile documentation built on May 11, 2019, 6:25 p.m.