Difference between revisions of "Talk:Sequence Alignments Gaucher Disease"
From Bioinformatikpedia
Rackersederj (talk | contribs) (Created page with "Just out of interest (I'm not reviewing your page this week): How did you generate your Venn diagrams? I really like the way they look. --~~~~") |
Rackersederj (talk | contribs) |
||
(5 intermediate revisions by 3 users not shown) | |||
Line 1: | Line 1: | ||
− | Just out of interest (I'm not reviewing your page this week): How did you generate your Venn diagrams? I really like the way they look. |
+ | Just out of interest (I'm not reviewing your page this week): How did you generate your Venn diagrams? I really like the way they look. |
+ | * We made use of [http://bioinformatics.psb.ugent.be/webtools/Venn this] online tool. |
||
+ | |||
+ | I see, you're not finished with the alignment part yet, but a few comments: |
||
+ | |||
+ | * I'm not sure about your evalutation of the hit list in pdb: You only report the overlap but don't use them as test set? |
||
+ | ** To which extend should we use the PDB hits as test set? Do you mean that we should have done a ROC analysis? As I wrote in the wiki, we would have needed a uniform test set for HHblits and blastpgp for being able to compare the different methods thoroughly. Another point is, that I do not really known how to classify the PDB hits as true positives and false positives. Did you find a good solution for that? |
||
+ | *** Not really, it just sounded like you had one for PDB but didn't tell us. :) |
||
+ | * If I get the task description right, we are supposed to create 5 datasets for the alignments, as you have done. Only if this is not possible, 3 less strictly defined datasets can be used. |
||
+ | --[[User:Boidolj|Boidolj]] 18:38, 7 May 2012 (UTC) |
||
+ | * I already talked about this in the last meeting and I know we did not come to a conclusion but i really dont think one should write about topics which do not concern [[Sequence_Alignments_Gaucher_Disease|THIS topic]]. If you really want to tell us something about the BIG or BIG_80 database i think you should do it in a separate topic |
||
+ | * its rather difficult to read your sentences with the parameter settings as a plain string like 1e-9 |
||
+ | *the last table should be fairly interesting but its empty I'm afraid as is the discussion meaning 2.4 |
||
+ | --[[User:Hollizeck|Hollizeck]] 20:06, 7 May 2012 (UTC) |
||
+ | |||
+ | *Thank you :) --[[User:Rackersederj|Rackersederj]] 05:18, 8 May 2012 (UTC) |
Latest revision as of 06:18, 8 May 2012
Just out of interest (I'm not reviewing your page this week): How did you generate your Venn diagrams? I really like the way they look.
- We made use of this online tool.
I see, you're not finished with the alignment part yet, but a few comments:
- I'm not sure about your evalutation of the hit list in pdb: You only report the overlap but don't use them as test set?
- To which extend should we use the PDB hits as test set? Do you mean that we should have done a ROC analysis? As I wrote in the wiki, we would have needed a uniform test set for HHblits and blastpgp for being able to compare the different methods thoroughly. Another point is, that I do not really known how to classify the PDB hits as true positives and false positives. Did you find a good solution for that?
- Not really, it just sounded like you had one for PDB but didn't tell us. :)
- To which extend should we use the PDB hits as test set? Do you mean that we should have done a ROC analysis? As I wrote in the wiki, we would have needed a uniform test set for HHblits and blastpgp for being able to compare the different methods thoroughly. Another point is, that I do not really known how to classify the PDB hits as true positives and false positives. Did you find a good solution for that?
- If I get the task description right, we are supposed to create 5 datasets for the alignments, as you have done. Only if this is not possible, 3 less strictly defined datasets can be used.
--Boidolj 18:38, 7 May 2012 (UTC)
- I already talked about this in the last meeting and I know we did not come to a conclusion but i really dont think one should write about topics which do not concern THIS topic. If you really want to tell us something about the BIG or BIG_80 database i think you should do it in a separate topic
- its rather difficult to read your sentences with the parameter settings as a plain string like 1e-9
- the last table should be fairly interesting but its empty I'm afraid as is the discussion meaning 2.4
--Hollizeck 20:06, 7 May 2012 (UTC)
- Thank you :) --Rackersederj 05:18, 8 May 2012 (UTC)