This data comes from a real unpublished shotgun proteomics experiment with two control and three bait (experimental) samples. It has been shown that such quantative mass spectrometry data follows a similar error model as DNA microarray data [15], thus Cyber-T is an appropriate approach for analysis. The data file is tab-delimited. The data has been pre-processed with dNSAF normalization. NOTE: The Cyber-T webserver does not currently offer this as a normalization option. There is one header row. There is one label column, and then there are two control columns and then three experimental columns.
This performs a two-sample t-test using the Bayes-regularized variance estimates. No normalization is performed. PPDE analysis and multiple hypothesis testing correction are performed on the p-values.
This is equivalent to a standard t-test using empirical variances. No normalization is performed. PPDE analysis and multiple hypothesis testing correction are performed on the p-values.