Moderator: Kevin Blighe
Kevin Blighe ♦ 54k
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From The Emerald Isle.
Developer / Maintainer of Bioconductor packages:
Other packages:
LinkedIn: https://www.linkedin.com/in/clinicalbioinformatics/
Posts by Kevin Blighe
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Answer:
A: available genotyping data
... That's quite a large number. I don't believe any such dataset currently exists that is public, but they will exist in the future.
Alternatively, if 2504 individuals is sufficient for you, then just follow the first few steps here:
- https://www.biostars.org/p/335605/
There are also datasets supp ...
written 8 minutes ago by
Kevin Blighe ♦ 54k
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... It should be easy for you to parse the output file such that only the top hit is retained. ...
written 1 hour ago by
Kevin Blighe ♦ 54k
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... Can you please link us to an example of a 'genetic marker frequency plot' ? ...
written 1 hour ago by
Kevin Blighe ♦ 54k
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... sinha.puja, to be fair, if you want help with something like this, then you need to post the exact code that you have been using, and also paste samples of the data that you currently have. You have not even provided a screenshot of what you are seeing on your screen. ...
written 15 hours ago by
Kevin Blighe ♦ 54k
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... The idea is still the same for using just the normalised expression levels, i.e., the beta coefficient represents the change between cases / controls based on 1-unit increase in your expression levels.
The interpretation of the output would indeed be easier if you converted your expression levels i ...
written 1 day ago by
Kevin Blighe ♦ 54k
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... Each will have advantages in different contexts, just like p-value adjustment methods. If you are unsure, then just use the default values. ...
written 1 day ago by
Kevin Blighe ♦ 54k
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... Cross-posted on Bioconductor: https://support.bioconductor.org/p/128388/ ...
written 1 day ago by
Kevin Blighe ♦ 54k
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... Fortunately or unfortunately, learning how to get data into the correct format is one of the most common things that you will do as a bioinformatician. In your situation, you should first obtain a vector of all files (`list.files()`) and then read in the information via `read.table()`, `fread()`, or ...
written 1 day ago by
Kevin Blighe ♦ 54k
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... There are many different combinations of `algorithm` and `statistic`, and I admit that I have not fully explored these. Is the problem that your enrichment p-values are not reaching statistical significance (p<0.05)? ...
written 1 day ago by
Kevin Blighe ♦ 54k
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... I have tidied it via the `101 010` button ...
written 1 day ago by
Kevin Blighe ♦ 54k
Latest awards to Kevin Blighe
Good Answer
3 days ago,
created an answer that was upvoted at least 5 times.
For A: Alternate nucleotide is more frequent than reference nucleotide. OMG I'm dizzy.
Teacher
6 days ago,
created an answer with at least 3 up-votes.
For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Appreciated
11 days ago,
created a post with more than 5 votes.
For Determine % of reference genome covered by aligned SAM/BAM
Teacher
15 days ago,
created an answer with at least 3 up-votes.
For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Teacher
15 days ago,
created an answer with at least 3 up-votes.
For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Good Answer
21 days ago,
created an answer that was upvoted at least 5 times.
For A: Building a predictive model by a list of genes
Good Answer
22 days ago,
created an answer that was upvoted at least 5 times.
For A: Automatic Outlier Detection for RNA-seq data
Appreciated
22 days ago,
created a post with more than 5 votes.
For PCAtools: everything Principal Components Analysis
Teacher
23 days ago,
created an answer with at least 3 up-votes.
For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Teacher
26 days ago,
created an answer with at least 3 up-votes.
For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Good Answer
28 days ago,
created an answer that was upvoted at least 5 times.
For A: Automatic Outlier Detection for RNA-seq data
Appreciated
28 days ago,
created a post with more than 5 votes.
For PCAtools: everything Principal Components Analysis
Teacher
29 days ago,
created an answer with at least 3 up-votes.
For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Teacher
5 weeks ago,
created an answer with at least 3 up-votes.
For A: Drug resistant vs. Drug sensitive data retreival from TCGA
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: Drug resistant vs. Drug sensitive data retreival from TCGA
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