normalizeCel: Normalize CEL Files

In yduan004/signatureSearchData: Datasets for signatureSearch package

Normalize CEL Files

Description

Function processes the CEL files from each chip type (three for CMap2 data) separately using the MAS5 normalization algorithm. The results will be written to subdirectores (under a data parent directory) that are named after the chip type names. To reduce the memory consumption of this step, the CEL files are processed in user definable batch sizes. For details on the overall workflow, please consult the vignette of this package. The normalization takes about 10 hours without parallelization. To save time, this process can be easily accelerated on a computer cluster.

Usage

normalizeCel(chiptype_list, batchsize = 300, rerun = TRUE)

Arguments

chiptype_list	list, storing CEL files in each chiptype
batchsize	number of CEL files to import and to normalize at once
rerun	TRUE or FALSE, whether to run the function

Value

Files storing normalized expression values in matrix, here one matrix file per chip type

Examples

# chiptype_list <- split(names(chiptype), as.character(chiptype))
normalizeCel(chiptype_list, rerun=FALSE)

yduan004/signatureSearchData documentation built on April 7, 2023, 4:12 a.m.