Moderator: Jean-Karim Heriche

Reputation:
7,690
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Trusted
Location:
EMBL Heidelberg, Germany
Website:
http://jkh1.github.io/
Last seen:
3 hours ago
Joined:
5 years, 7 months ago
Email:
h******@embl.de

Posts by Jean-Karim Heriche

<prev • 990 results • page 1 of 99 • next >
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Answer: A: How can I know when a pathway was included in Reactome?
... The genes to pathway membership information is available in the [downloadable mapping files][1]. Just select the file with the identifiers that suit you, e.g. for EnsEMBL IDs, use [this file][2]. EDIT: You can also use the pathway browser to navigate to your pathway then select the molecules tab ...
written 3 hours ago by Jean-Karim Heriche7.7k
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Comment: C: RNA-seq enrichment analysis with only one sample
... Let's say you've selected 10 genes from your data using whatever criterion. You can now count how many of these 10 genes are orthologs of, for example, bear hibernation genes. Let's say you find 3. The hypergeometric distribution can tell you how likely it is to find 3 genes of interest in a group o ...
written 3 hours ago by Jean-Karim Heriche7.7k
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Comment: C: A question on microarray-based validation study
... I don't know how arraymining.com works but from what you write, it seems to me that you can't reapply an already trained classifier. I would suggest to do the analysis yourself. For example in R, empirical Bayes statistics are available in the limma package and SVM in the kernlab package. ...
written 3 hours ago by Jean-Karim Heriche7.7k
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Answer: A: Training a classifier to recognize cancer biopsy images.
... Try the [The Cancer Imaging Archive (TCIA)][1]. [1]: http://www.cancerimagingarchive.net/ ...
written 20 hours ago by Jean-Karim Heriche7.7k
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Answer: A: RNA-seq enrichment analysis with only one sample
... Enrichment analysis is performed on sets. So if you can define some sets of genes in your data, you can test whether these sets are enriched in some genes known to be involved your process of interest using for example the hypergeometric distribution. ...
written 20 hours ago by Jean-Karim Heriche7.7k
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Answer: A: A question on microarray-based validation study
... Unless I misunderstand something, I don't see anything wrong in using the classifier you've trained on one data set to classify another similar data set. This is the best test of the robustness of the classifier. If it performs well on an independent data set then it is probably robust. If not, this ...
written 20 hours ago by Jean-Karim Heriche7.7k
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Comment: C: I need to understand this image
... A quick look at the [wikipedia article on differential evolution][1] makes me think that this is not what you're implementing. For example, I don't see your starting population nor any crossover operator. I am sorry but I don't have time now to try and understand your code and understand the type of ...
written 7 days ago by Jean-Karim Heriche7.7k
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Comment: C: I need to understand this image
... Sorry I am familiar neither with this kind of algorithm nor with Matlab. ...
written 8 days ago by Jean-Karim Heriche7.7k
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Comment: C: WGCNA error: Co-expression similarity and adjacency in Network Creation
... The error message suggests that some internal function doesn't like to work with integers, most likely you're working with count data. See point 4 of the [WGCNA FAQ][1]. [1]: https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/faq.html ...
written 8 days ago by Jean-Karim Heriche7.7k
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Answer: A: Swiss-Prot human count from the archives
... Old release notes have protein numbers by species. They can be found [here][1]. EDIT: All stats can be found [here][2]. [1]: http://www.ebi.ac.uk/uniprot/TrEMBLdocs/old_trembl_rel_notes.html [2]: http://www.uniprot.org/statistics/ ...
written 8 days ago by Jean-Karim Heriche7.7k

Latest awards to Jean-Karim Heriche

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Teacher 11 days ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
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Popular Question 9 weeks ago, created a question with more than 1,000 views. For Heatmaps in R
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Scholar 10 weeks ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
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Scholar 4 months ago, created an answer that has been accepted. For A: GO term enrichment
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Scholar 5 months ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers

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