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closeCriteria for the best algorithm
Posted by PLOS_CompBiol on 26 Feb 2008 at 15:39 GMT
Originally submitted as a Reader Response on 18th February 2008
(1) I thank to the author for this useful article. I was just wondering if there is any criteria to tag a particular algorithm as "the best" (as mentioned at few places in the article). Is there any rigorous comparative study for the available algorithms for tiling array analysis? If there is, I would love to go through it.
(2) I also wish to mention couple of well cited and popular algorithms for tiling array analysis, these are Chipotle (24 citations) and Tilemap (36 citations). These appears to be omitted from the present article.
(3) In my opinion, the basic requirement for any tiling array experiment is to fish out the true signals from background noise and most of the "rolling mean" and HMM based algorithms does that job very well. In such scenario, we do not expect separate algorithms for ChIP-chip, MeDIP,DNase-chip or even 4C.
Submitted by: Kuljeet Sandhu
E-mail: kuljeet.singh@ebc.uu.se
Occupation: PhD Scholar
Uppsala University
RE: Criteria for the best algorithm
PLOS_CompBiol replied to PLOS_CompBiol on 26 Feb 2008 at 15:41 GMT
Originally submitted as a Reader Response on 18th February 2008
To see the criteria for the best algorithm, please check out:
http://www.genome.org/cgi...
ChIPOTle made predictions after the key release and it still did not give the best results, so it was not included in the paper above.
TileMap was not tested in the spike-in study, but a comparative study was conducted at:
http://www.pnas.org/cgi/c...
Thanks!
Submitted by: X. Shirley Liu
E-mail: xsliu@jimmy.harvard.edu
Occupation: Associate Professor
Dana-Farber Cancer Institute, Harvard School of Public Health
RE: RE: Criteria for the best algorithm
PLOS_CompBiol replied to PLOS_CompBiol on 06 Mar 2008 at 10:57 GMT
Originally submitted as a Reader Response on 26th February 2008
Huge thanks to the author for providing useful link, seems to be much recent (Feb 7, 2008) than author's original article (Oct 26, 2007)
Submitted by: Kuljeet sandhu
E-mail: kuljeet.singh@ebc.uu.se
Occupation: PhD Scholar
Uppsala University