Moderator: Jean-Karim Heriche
Jean-Karim Heriche ♦ 20k
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- EMBL Heidelberg, Germany
- Website:
- http://jkh1.github.io/
- Last seen:
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- Joined:
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- Email:
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Posts by Jean-Karim Heriche
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... If you're going to use R to apply supervised machine learning algorithms, I would suggest to look into the [caret package][1]. It has a createDataPartition() function for splitting data.
[1]: https://topepo.github.io/caret/ ...
written 2 hours ago by
Jean-Karim Heriche ♦ 20k
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... Without knowing anything about the structure of the data and how it's going to be processed, the only advice that can be given is to use a random split. For machine learning applications, it's common to use 67-80% of the data for training and the rest for testing. Both the training set and the test ...
written 10 hours ago by
Jean-Karim Heriche ♦ 20k
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... The suggestion is make a histogram of all your p-values and if the shape of that histogram doesn't indicate any issue then apply a correction using all p-values. ...
written 10 hours ago by
Jean-Karim Heriche ♦ 20k
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... Filtering data before statistical testing as a means to increase sensitivity is often done but is tricky if one wants to still adequately control the false positive rate. See for example this [paper][1]. I would hesitate to do it and would only consider it based on independent information, not on an ...
written 1 day ago by
Jean-Karim Heriche ♦ 20k
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... > But the single cluster is not breaking
because the members are very close to each other in PCA space (did you try using more than two components for clustering?), meaning that they can't be distinguished based on genetic variability as captured by your data. Without access to the data, it's di ...
written 1 day ago by
Jean-Karim Heriche ♦ 20k
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... Late answer that might still be useful. A recurrent issue with ontologies is that terms relevant to the question at hand are often at different levels of the ontology and many branches of the ontology may be irrelevant. One way to deal with this is to use a slim ontology, i.e. a subset of the ontolo ...
written 1 day ago by
Jean-Karim Heriche ♦ 20k
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Comment:
C: How to discover novel piRNA?
... Search for papers. Also consider that piRNAs are one type of non-coding RNAs.
...
written 6 days ago by
Jean-Karim Heriche ♦ 20k
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... Without seeing the file content, one can only guess at what the problem is although most likely it is a data format issue. Check that your file conforms to what's expected by the readMappings function, i.e. columns are tab-separated and the first one contains gene IDs, the second one a comma-separat ...
written 7 days ago by
Jean-Karim Heriche ♦ 20k
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... 1- You can retrieve the whole ontology from the [download page of Gene Ontology web site][1] or use the [Bioconductor package GO.db][2], e.g.
library(GO.db)
GO <- as.list(GOTERM)
my.term <- GO$`GO:0000001`@Term
[1]: http://geneontology.org/docs/download-ontology/
[2]: http: ...
written 11 days ago by
Jean-Karim Heriche ♦ 20k
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... Yes I believe this is the wrong place to ask. First you're creating an answer to a question without addressing that question (use comments to add to the discussion without answering a question, answers are for answers). Second you're asking a different question so you should create your own question ...
written 11 days ago by
Jean-Karim Heriche ♦ 20k
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