LumiBatch2GEOarchive: Convert a LumiBatch into a GEOarchive formatted file

In drmjc/microarrays: A collection of microarray and genomic helper code.

Description

To upload Illumina gene expression data to GEO requires a specific format: http://www.ncbi.nlm.nih.gov/geo/info/geo_illu.html
Briefly, you need both the unnormalised, and normalised data, both of which must include the expression level, and detection p-val for each probe, using ILMN_ -style probe ID's. LumiBatch objects conform to this style already.

Usage

  LumiBatch2GEOarchive(x, file, ids = NULL,
    round.digits = 5)

Arguments

x	a LumiBatch object; or
file	the path to a GenomeStudio TXT file. it should end in tsv or txt.
ids	an optional vector of probe ID's. Default=NULL to use the featureNames within x. See Details.
round.digits	The number of digits to round the data to. No point exporting anything much more precise than 4-5 decimal places. Set to NULL to skip this.

Value

nothing. it writes a tab-delimited file.

Probe naming

Due to there being a number of different naming conventions for Illumina probes (see ?preprocess.illumina.idat) the probe ID style can differ depending on the probeID type selected either by Illumina's GenomeStudio, or one of the lumi methods provided by this package: preprocess.illumina.idat, lumiR.idat. If your probe ID's differ from the “ILMN_” style, then you will either need to convert them to ILMN_ style, using an appropriate probe-level annotation package, eg illuminaHumanv4.db, or find a GEO Platform which uses your identifiers.

This function pulls the expression levels and detection pvalues from a LumiBatch object and writes an xls file.

ids argument

If you'd like to reorder, or subset the rows in the output, set the ids argument to be a character vector of probe ID's. In addition, ids may contain probes that are not present in featureNames(x) – in this case these probes will be in effect added to x, and exported as “null”'s. This is a bit of a hack, because it's hard to add missing probes to a LumiBatch object retrospectively.

Note

This shold work for ExpressionSet objects, but that's currently untested.

Author(s)

Mark Cowley, 2012-03-29

Examples

## Not run: 
LumiBatch2GEOarchive(x.raw, "geosub-unnorm.xls")
LumiBatch2GEOarchive(x.norm, "geosub-norm.xls")

## End(Not run)

drmjc/microarrays documentation built on May 15, 2019, 2:26 p.m.