makeNanoStringSetFromEset: Convert NanoString ExpressionSet to NanoStringSet

In calebclass/NanoTube: An Easy Pipeline for NanoString nCounter Data Analysis

Convert NanoString ExpressionSet to NanoStringSet

Description

Convert ExpressionSet from processNanoStringData to a NanoStringSet for use with the NanoStringDiff package.

Usage

makeNanoStringSetFromEset(eset, designs = NULL)

Arguments

eset	NanoString data ExpressionSet, from processNanostringData
designs	Design matrix. If NULL, will look for "groups" column in pData(eset).

Value

A NanoStringSet for NanoStringDiff

Examples

# Example data
example_data <- system.file("extdata", "GSE117751_RAW", package = "NanoTube")
sample_data <- system.file("extdata", "GSE117751_sample_data.csv", 
package = "NanoTube")

# Load data without normalization
dat <- processNanostringData(nsFiles = example_data,
                     sampleTab = sample_data, groupCol = "Sample_Diagnosis",
                     normalization = "none")
                     
# Convert to NanoStringSet
dat.ns <- makeNanoStringSetFromEset(dat)

calebclass/NanoTube documentation built on Nov. 21, 2023, 12:31 p.m.