inst/models/diff.R

In iaradsouza1/MicroarrayMethods: Provide methods for microarray analysis

# Differential expression analysis ----------------------------------------
library(MicroarrayMethods)

# Define function arguments
celfiles_path <- "~/Área de Trabalho/exp1/"
pheno_data <- "samples.txt"
sep <- "\t"
group <- "group"
type <- NULL
batch <- "batch"
report_output <- "~/Área de Trabalho/QC12312.html"
dataset <- "hsapiens_gene_ensembl"
platform <- "affy_hg_u133_plus_2"
ref_col <- "hgnc_symbol"
contrasts <- c(s8xs0 = "shOTX2_8-shOTX2_0", s16xs8 = "shOTX2_16-shOTX2_8", s24xs16 = "shOTX2_24-shOTX2_16",
               s48xs24 = "shOTX2_48-shOTX2_24", s96xs48 = "shOTX2_96-shOTX2_48")

# Quality control report
create_report(celfiles = celfiles_path,
              pheno_data = pheno_data,
              sep = sep,
              components = c(1,2),
              group = group,
              batch = batch, output_file = report_output)

# Import and normalize
eset <- import_norm(celfiles_path = celfiles_path, pheno_data = pheno_data, sep = sep)

# Get probes annotation
feature_data <- get_annotation(dataset = dataset, platform = platform)

# Set annotation into eset and remove promiscuous probes and dual notations
eset <- set_fdata(eset, feature_data,
                  probe_col = platform,
                  ref_col = ref_col,
                  rm_probes = TRUE)

# Differential expression
delimma <- diff_exp(eset, contrasts, method = "global", adjust.method = "BH", p.value = 0.001, degenes_only = T)