Moderator: Jean-Karim Heriche

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EMBL Heidelberg, Germany
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http://jkh1.github.io/
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Posts by Jean-Karim Heriche

<prev • 2,345 results • page 1 of 235 • next >
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Comment: C: Trainng and validation set selection
... 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 Heriche20k
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Comment: C: Trainng and validation set selection
... 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 Heriche20k
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Comment: C: Correlation test for multiple variables and adjusted p values
... 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 Heriche20k
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Answer: A: Correlation test for multiple variables and adjusted p values
... 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 Heriche20k
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Comment: C: PCA cannot separate different breeds
... > 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 Heriche20k
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Answer: A: grouping gene ontology parent-child terms
... 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 Heriche20k
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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 Heriche20k
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Comment: C: Importing eggnog annotations into topGO or similar?
... 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 Heriche20k
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Answer: A: associate GO ID with GO description
... 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 Heriche20k
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Comment: C: Run a GO analysis for an non-model organism with annotation file
... 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 Heriche20k

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Epic Question 3 days ago, created a question with more than 10,000 views. For Heatmaps in R
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Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
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Scholar 6 weeks ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers

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