The mRNA and cDNA sequences in the dataset were removed using the program EST-trimmer (http://pgrc.ipk-gatersleben.de/misa/download/est_trimmer.pl).
Moreover, in order to avoid overestimating the current method, any sequence in the two subsets that has ≥40% pairwise sequence identity to any sequence in benchmark dataset or expanded benchmark dataset was removed using CD-HIT program [ 38].
Batch effects of dataset, plate, array and position were removed using ComBat [ 43].
To lower the redundancy in the dataset, low-coverage artifacts or redundancies were removed using the CD-HIT-EST program (Li and Godzik 2006) with an identity threshold of 95%.
The eight datasets were then combined, and batch effects were removed using the BFRM algorithm (Yuwanita and Andrechek, Unpublished).
The duplicated reads were removed using picard (versions 1.106, 1.106, and 2.5.0 for the datasets 1, 2, and 3, respectively).
The ACIS calibration team has responded to an internal request to upgrade two of the ACIS-8(S) blank-sky background files due to the presence of streaks in the datasets that may now be removed using the latest destreak software (actually released in CIAO 4.0 in December 2007).
The technical redundancy in the dataset (perfect sequence duplication) was removed using the NCBI nrdb program, included in the downloadable Blast suite.
In this study, artifact-free EEG datasets are used in which the artifacts are removed using ICA.
Note: 3 outlying "slow" samples (biological replicates) within the LC-MS/MS dataset were removed following quality control using principal components analysis (data not shown).
