Moderator: Jean-Karim Heriche

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EMBL Heidelberg, Germany
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Posts by Jean-Karim Heriche

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Comment: C: PANTHER gene ontology - is the bonferroni correction important?
... 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 Heriche12k
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Comment: C: PANTHER gene ontology - is the bonferroni correction important?
... 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 Heriche12k
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Comment: C: Assigning gene ontologies to a big set of protein sequences
... 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 Heriche12k
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Comment: C: Assigning gene ontologies to a big set of protein sequences
... 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 Heriche12k
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Answer: A: Is it fair to compare the significance of overlap of 2 different sized gene sets
... 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 Heriche12k
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Comment: C: PANTHER gene ontology - is the bonferroni correction important?
... 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 Heriche12k
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Answer: A: PANTHER gene ontology - is the bonferroni correction important?
... 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 Heriche12k
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Answer: A: What kinds of annotation database can be used for biological enrichment?
... 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 Heriche12k
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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 Heriche12k
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Comment: C: Comparing proteomes in which most protein abundances differ
... 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 Heriche12k

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