lumi (version 2.24.0)

produceGEOPlatformFile: Produce GEO Platform Submission File in SOFT format

Description

Produce GEO Sample Submission File in SOFT format based on the provided LumiBatch object and Illumina ID Mapping library

Usage

produceGEOPlatformFile(x.lumi, lib.mapping = NULL, nuIDMode = TRUE, includeAllChipProbe=FALSE, fileName = "GEOPlatformFile.txt")

Arguments

x.lumi

The LumiBatch object keeping all probes

lib.mapping

The Illumina ID Mapping library, e.g., "lumiHumanIDMapping"

nuIDMode

Determine whether producing the platform indexed by nuID

includeAllChipProbe

Determine whether including all probes in the Manifest file or just the probes used in the x.lumi object

fileName

Filename of the GEO Platform File name

Value

Save the result as a text file in SOFT platform submission format.

Details

The function produces the GEO platform submission file based on the chip information kept in the Illumina ID Mapping library (specified by lib.mapping parameter). The determination of chip type will be automatically done by selecting the best matching of the probe IDs with individual chips.

References

http://www.ncbi.nlm.nih.gov/projects/geo/info/soft2.html

See Also

produceGEOSubmissionFile

Examples

# data(example.lumi)
# produceGEOPlatformFile(example.lumi, lib.mapping='lumiHumanIDMapping')