[Ngasp-help] Re: nGASP manuscript

[Tomas Vinar]

Hello,

The paper is a very nice summary of the experiment. I have very few comments
and corrections.

Corrections in Table 1:
- Augustus entry: there is only one author (Stanke), so writing "Stanke et
al." is perhaps not the best
- ExonHunter entry: there are two authors, so it would be nicer to write
Brejova and Vinar (instead of Vinar et al.), or at least please change this
to Brejova et al.

Other comments:

- in abstract: "There was a tie for the third place..." -> this sentence
implies that cross-species gene finding does not work in C. elegans. That
may be a very sensitive point with some referees, and I don't feel that the
corresponding section in the "results" gives good enough discussion on this
subject. I would remove the sentence from the abstract as to not immediately
make it a discussion point, especially if better analysis cannot be made.

- in results: comparisons between EGASP and nGASP numbers. I am not sure
that the direct comparison of numbers between EGASP and nGASP is a good
idea. From various experiments in past, it seems clear that the absolute
numbers in Sn and Sp can change dramatically depending on particular testing
set, even within species. Considering that there are some substantial
differences in methodologies between EGASP and nGASP, while comparing the
absolute numbers can give some information on general trends, I don't think
some of the conclusions can be supported by the data, especially ones
derived from comparison of gene level sensitivities and specificities.

- short table giving overview of numbers of genes/exons/bases and basic
comparison of EGASP and nGASP data sets (e.g., exon lengths, intron lengths,
exon numbers, etc.) would be useful

- Table 3: Why gene Sn is given only to 1 decimal digit, while all the other
numbers are given to 2 decimal digits? Also, I am not sure how much it is
justified to give the data to 2 decimal digit precision, since  0.01 is not
likely to be anywhere near to statistically significant difference in any of
the measures

On Wed, Jul 16, 2008 at 1:26 PM, Dr. Tristan J. Fiedler <fiedler at fit.edu>
wrote:

> Dear nGASP Participants,
>
> We thank you again for your participation in nGASP.
>
> The nGASP analysis team has now written up the results of nGASP
> as a paper, which we plan to submit to BMC Bioinformatics.
>
> As agreed, we are sending you a copy of the draft manuscript
> for your perusal before submission.
>
> We would be very grateful if you can let us know if you have any
> major comments on the draft manuscript by Thursday 24th July.
>
> Comments may be sent to ngasp-help at wormbase.org
>
> Yours sincerely,
>
> The nGASP analysis team.
>
>
>


-- 
--------------------------------------------------------------------------
Tomas Vinar, Postdoctoral Researcher
Biological Statistics and Computational Biology
Cornell University
E-mail: tv35 at cornell.edu
Office: 169 Biotechnology Building
Work Phone: +1-607-255-7430
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/ngasp-help/attachments/20080722/930674a3/attachment.html>