# Set working directory for aroma and define chip set to work on now
setwd("F:\\aroma");

# Load the source code
source("Scripts/agronomicsTools01.r")

# Call the standard RMA analysis using agronomics1_TAIR9_gene.cdf and dynamically remove poor probes
AGRONOMICS1_RMA(experimentName = "TSU_1", Filter=TRUE, force = TRUE)

# Load results from AGRONOMICS1_RMA
load("reports\\TSU_2\\agronomics1\\agronomics1_TAIR9_gene_RMA.RData")
Signals <- theta
str(Signals)


# Call a more flexible function that can use any array / cdf. Note that this function does not filter out poor probes.

aromaRMA(experimentName = "TSU_1", dataChipType = "ATH1-121501", analysisChipType = "ATH1-121501")