norm_fc: Normalize all NanoString .RCC files in a directory

In sgrote/NanoStringNormalizeR: Normalize all NanoString .RCC files in a directory

Description

Wrapper for NanoStringNorm to be applied to all .RCC files in the input directory

Usage

norm_fc(input_folder, house_genes)

Arguments

input_folder	character(), folder with .RCC files and/or subfolders with .RCC files for each run
house_genes	character() vector with housekeeping genes to use for the normalization

Details

Normalization steps:
1. collect and merge all .RCC files 2. positive control normalization using NanoStringNorm(..., CodeCount = "geo.mean") 3. flag samples with Positive Control normalization factor > 3 or < 0.3 4. compute background threshold (mean + 2 * sd of negative controls) 5. houskeeping gene normalization using NanoStringNorm(..., SampleContent = "housekeeping.geo.mean") 6. flag samples with sampleContent normalization factor > 10 or < 0.1 7. mask samples

Value

invisible NULL
Side effects: Creates folder 'results' in input_folder, containing:
* a table with normalized NanoString data
* a table with flagged samples (unusual normalization factors)
* a table with ratios for target samples
* a table with ratios for reference samples (mvp-samples)
* a table with fold-changes
* a table with fold-changes for reference samples (mvp-samples)
* a table with ratios compared to all non-mvp-samples
* a table with fold-changes compared all non-mvp-samples

Author(s)

Steffi Grote

References

NanoString Gene Expression Data Analysis Guidelines (MAN-C0011-04)
https://cran.r-project.org/web/packages/NanoStringNorm/vignettes/NanoStringNorm_Introduction.pdf

sgrote/NanoStringNormalizeR documentation built on Dec. 30, 2020, 7:45 p.m.