invariant.probe.norm: Normalize data using invariant probes

In uclahs-cds/public-R-NanoStringNormCNV: Helper Functions to Normalize NanoString CNV Data

Normalize data using invariant probes

Description

Normalize data using invariant (INV) probes to control for differences in sample input

Usage

invariant.probe.norm(nanostring.data, phenodata = NULL)

Arguments

nanostring.data	A gene by sample data-frame of NanoString counts (can either be raw or have already been normalized by a separate normalization technique). First three column names must be 'CodeClass', 'Name', and 'Accession', followed by sample IDs
phenodata	A data-frame of sample annotation with fields 'SampleID' and 'Type' (specifying whether sample is 'Tumour' or 'Reference'). Recommended to use output of load.phenodata. Defaults to NULL

Details

NanoString counts are multiplied by a normalization factor (mean(mean INV probe count of each sample) / mean INV probe count of given sample). This procedure is not carried out on 'Positive', 'Negative' and 'RestrictionSite' code class probes.
Be aware that invariant probe counts of < 100 signify low DNA input. This may lead to unreliable CNA calls, especially if the low counts are in the reference samples!
This function is called from normalize.global and normalize.per.chip, if invariant probe normalization is requested.
Diagnostic plots are saved as tiff files to the working directory.

Value

A gene by sample data-frame of normalized counts, where the first three columns contain 'CodeClass', 'Name', and 'Accession' information

Author(s)

Cindy Yao and Emilie Lalonde

References

See NanoString website for PDFs on analysis guidelines: https://www.nanostring.com/support/product-support/support-documentation

The NanoString assay is described in the paper: Fortina, P. & Surrey, S. Digital mRNA profiling. Nature Biotechnology 26, 293-294 (2008).

See Also

NanoStringNorm::sample.content.normalization

Examples

## Not run: 
	# load raw data
	data(NanoString.DNA.raw);
	data(PhenoData)

	# normalize
	normalized.data <- invariant.probe.norm(
		nanostring.data = NanoString.DNA.raw,
		phenodata = PhenoData
		);	

## End(Not run)

uclahs-cds/public-R-NanoStringNormCNV documentation built on May 31, 2024, 9:09 p.m.