microarray_limma_differential: GEO dataset analysis by limma.

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

GEO dataset analysis by limma.

Description

GEO dataset analysis by limma.

Usage

microarray_limma_differential(
  exp,
  group,
  check.log2 = TRUE,
  normalizeBetweenArrays = TRUE
)

Arguments

normalizeBetweenArrays

Value

Normalized expression data.frame and differential analysis result

Examples

# Code from GEO2E. Thanks
library(dplyr)
GSE32575 <- loonR::download.geo.dataset("GSE32575", "GPL6102")
control <- GSE32575$phenotype %>%
  filter(characteristics_ch1.2 == "disease state: obese before bariatric surgery") %>%
  pull(geo_accession)
experiment <- GSE32575$phenotype %>%
  filter(characteristics_ch1.2 == "disease state: obese after bariatric surgery") %>%
  pull(geo_accession)
exp.df <- GSE32575$expression[, c(control, experiment)]
group <- rep(c("Before", "After"), c(length(control), length(experiment)))
loonR::microarray_limma_differential(exp.df, group)

ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.