Errata Corrige for PaGE publication
Errata Corrige and Notes to the original PaGE paper (Bioinformatics, 16(8))
The argument given in section Methods and Algorithm to support the approximation (3) to the false positive rate is stated in the paper with a confusing notation. A revised argument can be found in section 3 of the CAMDA'00 paper downloadable below.
Note on section Results: Comparison
with standard methods.
Revised Algorithms: The PaGE algorithm has evolved significantly since the time of the original publication.
- The algorithm employed by versions 2.1 of PaGE was a revised version of the one provided in Figure 2 of the original paper. Among other things, it no longer performed data clean-up (through "minimum useful values"). This because data clean-up very much depends on the data at hand and it is best if left to the user, who knows the details of the experiments and the quantification software utilized. Also, step 8 of the PaGE 2.1 algorithm corrected an oversight in the original paper. For a pdf file containing the PaGE 2.1 Algorithm, click here.
- The algorithm used in version 5.0 and higher, corresponding to the software currently made available, differs even more drastically from the original algorithm, as illustrated in the technical manual. In the most recent algorithm permutation techniques are utilized and different statistics can be employed. Still in common with the original paper are the intent of controlling the FDR and the output produced in terms of easily interpretable patterns with integer symbols.