Moderator: Jean-Karim Heriche
Jean-Karim Heriche ♦ 12k
- Reputation:
- 11,820
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- Location:
- EMBL Heidelberg, Germany
- Website:
- http://jkh1.github.io/
- Last seen:
- 2 days, 6 hours ago
- Joined:
- 6 years ago
- Email:
- h******@embl.de
Posts by Jean-Karim Heriche
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... You know to what degree it's conservative: you get an upper bound on the p-value. There is no method better than another for multiple testing adjustment. Whichever you choose will give you a trade-off between false positives and false negatives. People are usually concerned with the removal of false ...
written 3 days ago by
Jean-Karim Heriche ♦ 12k
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... I agree that in general, one should make sure assumptions hold when applying statistical tests but
I think you're missing the point of what conservative means. It means that the p-value you obtain is guaranteed to be greater than the real one.
When the assumptions are met, the FDR gives you the prop ...
written 5 days ago by
Jean-Karim Heriche ♦ 12k
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... If applicable in your case, you could transfer annotations by orthology or simply by homology. It seems that the throughput in your case could be a matter of parallelization. ...
written 5 days ago by
Jean-Karim Heriche ♦ 12k
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... As far as I can tell, IDs of the form PTHR24242 refer to Panther families. Panther families are defined by Panther and don't necessarily match other resources definitions. If you need GO annotations then use GO terms, not something else that may or may not have a GO equivalent. ...
written 5 days ago by
Jean-Karim Heriche ♦ 12k
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... The overlap between two sets follows a hypergeometric distribution. When doing a hypergeometric test, the various sizes are taken into account so because Fisher's exact test is based on the hypergeometric distribution, it also takes sample size into consideration. Note that for this (and the Chi-squ ...
written 6 days ago by
Jean-Karim Heriche ♦ 12k
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... You're right that the corrections assume independence of the tests. However, the Bonferroni correction in the case of non-independence is over-conservative (see for example [here][1]) so it's OK to use if you're fine with that. The same goes for the Benjamini-Hochberg FDR correction, see this [paper ...
written 6 days ago by
Jean-Karim Heriche ♦ 12k
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... It is as described in what you posted from the Panther website. You need correction for multiple testing to control for significant results that would happen by chance (which would be considered false positives). So there is a trade-off, reduce the number of false positives and you increase the numb ...
written 6 days ago by
Jean-Karim Heriche ♦ 12k
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... As already pointed out, genes are annotated with various types of information. Which one you use depends on the question you're trying to address. If you're asking something about cellular function then you want to use functional type of annotations. If your question is more about structure then you ...
written 7 days ago by
Jean-Karim Heriche ♦ 12k
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Comment:
C: Problem using biomaRt
... This looks like a problem with the package installation. Remove it and try to install it again. ...
written 7 days ago by
Jean-Karim Heriche ♦ 12k
0
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... The summed abundance is not related to the absolute total amount if you express it as proportion of the total. The sum of all proteins will be 100%, irrespective of what amount you started with. In this way, you only get relative information. If preserving absolute information on abundance is necess ...
written 7 days ago by
Jean-Karim Heriche ♦ 12k
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For A: Bonferonni Correction for mostly overlapping enhancers
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For A: Bonferonni Correction for mostly overlapping enhancers
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For C: Is Software Development a key part of Bioinformatics?
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For C: How to make sure there is no duplicate sequence in a fasta file?
Scholar
16 days ago,
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For A: Bonferonni Correction for mostly overlapping enhancers
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For A: Rnai Screening Data Repositories?
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20 days ago,
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For A: Bonferonni Correction for mostly overlapping enhancers
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For A: Rnai Screening Data Repositories?
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For C: How to make sure there is no duplicate sequence in a fasta file?
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26 days ago,
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For A: Bonferonni Correction for mostly overlapping enhancers
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27 days ago,
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For A: Bonferonni Correction for mostly overlapping enhancers
Teacher
27 days ago,
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For A: Rnai Screening Data Repositories?
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5 weeks ago,
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For C: How to make sure there is no duplicate sequence in a fasta file?
Commentator
5 weeks ago,
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For C: How to make sure there is no duplicate sequence in a fasta file?
Teacher
5 weeks ago,
created an answer with at least 3 up-votes.
For A: Rnai Screening Data Repositories?
Scholar
5 weeks ago,
created an answer that has been accepted.
For A: Bonferonni Correction for mostly overlapping enhancers
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: Bonferonni Correction for mostly overlapping enhancers
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: Rnai Screening Data Repositories?
Commentator
7 weeks ago,
created a comment with at least 3 up-votes.
For C: How to make sure there is no duplicate sequence in a fasta file?
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: Rnai Screening Data Repositories?
Scholar
7 weeks ago,
created an answer that has been accepted.
For A: Bonferonni Correction for mostly overlapping enhancers
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7 weeks ago,
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For A: Rnai Screening Data Repositories?
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