Assessing the efficiency of dye-swap normalization to remove systematic bias from two-color microarray data

This page contains material related to the paper:

Sanchez-Cabo F, Cho KH, Hinds J, Wolkenhauer O
Assessing the efficiency of dye-swap normalization to remove systematic bias from two-color microarray data

In this paper, three different data sets were used to test the efficiency of dye-swap normalization. The complete data was normalized using different packages of the Bioconductor project and the filtered data using Arraynorm (www.genome.tugraz.at). To guarantee the reproducibility of the results, we provide here the code used to normalize each data set.

All files are contained in: suppl_mat.zip

• Self-self hybridization experiment (File called data_normalization_self, within the folder self-self)
• M.tuberculosis growth curve - Matlab code (Matlab files folder within TB data set folder) -R code (R functions file within the TB data set folder)
• Analysis of the yeast transcriptional repressors Mig1p and Mig2p (Files within the folder mig1mig2 data set. The file "normalizing_mig1mig2_lowess" should be renamed as "normalizing_mig1mig2")