positive.control.qc: Perform QAQC using positive controls

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

Perform QAQC using positive controls

Description

Positive control probes are compared to the expected positive control standard curve, as provided in the NanoString manual, y = 171.23x + 214.12. An R squared value of > 0.95 is expected for every sample and the user is warned if this is not satisfied.

Usage

	positive.control.qc(raw.data)

Arguments

raw.data

A gene by sample data-frame of raw NanoString counts for positive control probes. First three column names must be 'CodeClass', 'Name', and 'Accession', followed by sample IDs

Details

Determine the correlation between expected and observed positive control probe values

Value

A data-frame of R squared values by sample ID

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

make.positive.control.plot

Examples

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

	# run QC
	r.squared <- positive.control.qc(raw.data = NanoString.DNA.raw);

## End(Not run)

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