export.broad.res: Export a res file for GenePattern.

In drmjc/metaGSEA: Meta-analysis of GSEA analyses, including intra- and inter-experiment comparisons

Description

This requires a matrix of data (such as from RMA) and a matrix of calls, usually MAS5 calls of P/M/A. If you use Affymetrix ST arrays, you can generate DABG calls, then use dabg2calls

Usage

export.broad.res(data, calls, description = NULL, file, missing = "",
  unlog2 = TRUE)

Arguments

data	matrix of expression levels. If this is log base 2, then it will be unlog2ged. If you use any other log base, then unlog2 it yourself
calls	matrix of calls: P/M/A
description	a description for each ProbeSet. If NULL, then rownames of data will be used. if it doesn't have names, we assume it is the same length and in samre order as nrow(data) if it does have names, then only the relevant values will be extracted using the rownames(data) as the key.
file	the filename
missing	the value to write if there's any NA values
unlog2	logical: unlog the log-base-2 data?

Value

creates a res file

Author(s)

Mark Cowley, 2009-06-26

See Also

http://www.broadinstitute.org/cancer/software/genepattern/tutorial/gp_fileformats.html#res

drmjc/metaGSEA documentation built on Aug. 8, 2020, 1:53 p.m.