Moderator: Jean-Karim Heriche

Reputation:
10,690
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Trusted
Location:
EMBL Heidelberg, Germany
Website:
http://jkh1.github.io/
Last seen:
6 hours ago
Joined:
5 years, 11 months ago
Email:
h******@embl.de

Posts by Jean-Karim Heriche

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Answer: A: How can extract nucleotide frequency for position on aligned sequences in clusta
... You could use the [seqinr package for R][1]. First read in your alignment with the read.alignment() function then use the consensus() function with method="profile" to get a matrix of counts of each nucleotide at each position. [1]: https://CRAN.R-project.org/package=seqinr ...
written 10 hours ago by Jean-Karim Heriche11k
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Comment: C: why spectral clustering show a warning?
... > what's wrong As the message says, your graph is not fully connected or said another way, your graph has several connected components or to put it in plain English, your graph is composed of several subgraphs that are not connected to each other. You should identify what these subgraphs are. ...
written 1 day ago by Jean-Karim Heriche11k
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Comment: C: why spectral clustering show a warning?
... An affinity matrix is a similarity matrix. Your adjacency matrix is an affinity matrix because the edge weights represent similarity between the nodes. ...
written 1 day ago by Jean-Karim Heriche11k
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Comment: C: Bioconductor Graphite package : Cannot retrive pathways
... What's the version of graphite you're using ? Non-human data has only been made accessible from version 1.14. ...
written 2 days ago by Jean-Karim Heriche11k
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Comment: C: HeLa reference fasta
... Yes, you need to request access to the data from dbGAP. From what I've been told, requesting access is a pain and has to be done for each use of the data separately plus access authorization expires quickly and has to be renewed. My opinion is that if the HeLa genome sequence is of long term intere ...
written 2 days ago by Jean-Karim Heriche11k
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Comment: C: Fisher test for enrichment analysis
... > the aim is to check if other tumors come because of breast cancer surgery That's a different question for which you would need different data. ...
written 2 days ago by Jean-Karim Heriche11k
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Comment: C: Discussion Regarding P-Value
... There's no information to confirm what these p-values are. Saying they result from comparison with some probe is an assumption and even if true, you don't know what this probe was. So the only thing to do with these p-values is to ignore them. ...
written 2 days ago by Jean-Karim Heriche11k
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Comment: C: Discussion Regarding P-Value
... > ... which I am assuming the average gene expression values When it comes to data analysis, don't assume, be certain. If the data was generated with some sort of data management system in place, all necessary information should be available and not depend on the person having done the work to ...
written 2 days ago by Jean-Karim Heriche11k
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Comment: C: Discussion Regarding P-Value
... The clarifications have to come first from the data-generating side: - What are the expression values, what do they measure ? - What test was used to generate the p-values ? What was the null hypothesis ? To me, at the moment, you have a bunch of meaningless numbers. You can always compute a ...
written 2 days ago by Jean-Karim Heriche11k
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Answer: A: Fisher test for enrichment analysis
... If you're only interested in whether there's a difference in proportion of the two types of cancers between the two groups, then a chi-squared test or Fisher's exact test are appropriate and simpler. A logistic regression is possible but it would evaluate the cancer type as a function of the year, i ...
written 2 days ago by Jean-Karim Heriche11k

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Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
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