Moderator: Giovanni M Dall'Olio
Giovanni M Dall'Olio ♦ 26k
- Reputation:
- 25,710
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- London, UK
- Website:
- http://bioinfoblog.it/
- Twitter:
- dalloliogm
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- Last seen:
- 10 hours ago
- Joined:
- 8 years, 8 months ago
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Research Associate at the King's College of London. Interested in human population genetics and cancer.
Posts by Giovanni M Dall'Olio
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... Yes, it is directional but in many cases you don't really know which is the ancestral allele or not. In that case it is safer to get the absolute score, and determine whether there is selection between the two populations, without knowing which is the allele selected. Moreover people tend to calcula ...
written 1 day ago by
Giovanni M Dall'Olio ♦ 26k
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... I had trouble downloading the data in the past, luckily the help desk is always very useful and they will answer in a few hours.
In the end we managed to find another way to download the data using the cloud.
...
written 7 months ago by
Giovanni M Dall'Olio ♦ 26k
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... Explanation: your column is stored as factors
Solution1: as.integer(as.character(mycolumn))
Solution2: use stringAsFactors=F when reading the data ...
written 7 months ago by
Giovanni M Dall'Olio ♦ 26k
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Comment:
C: Boxplot in ggplot2
... This is good but I would use gather from tidyr. The package tidyr is the evolution of reshape2, and it contains more functions to massage data and reshape it for ggplot2/tidyverse. ...
written 10 months ago by
Giovanni M Dall'Olio ♦ 26k
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Comment:
C: p-value in GSEA
... Just a clarification: the p-values did not change because of the order of genes, but because of a different random number seed. Try running the same analysis on the same set without changing the order, and the p-values will be different again. ...
written 14 months ago by
Giovanni M Dall'Olio ♦ 26k
0
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Comment:
C: p-value in GSEA
... Moderator note: I've moved this from a comment to a reply, so it can be voted as a proper answer. ...
written 14 months ago by
Giovanni M Dall'Olio ♦ 26k
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... In my personal order of preference:
- Mygene.info http://mygene.info/ - can recognize many types of IDs automatically. When an Ensembl ID matches to multiple Entrez ID, they hacked a way to map to only the entrez id with the correct symbol
- HGNC Biomart http://biomart.genenames.org/ - HGNC is th ...
written 16 months ago by
Giovanni M Dall'Olio ♦ 26k
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1.6k
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Comment:
C: Poll: How many people have PyPy?
... Why would I need to have PyPy installed? ...
written 16 months ago by
Giovanni M Dall'Olio ♦ 26k
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... I agree with your comments - it seems something is wrong with the experiment, there it should not be so many NAs. The best thing to do would be to revise the design. ...
written 16 months ago by
Giovanni M Dall'Olio ♦ 26k
0
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934
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... how many rows do you have before and after adding the gene names? ...
written 16 months ago by
Giovanni M Dall'Olio ♦ 26k
Latest awards to Giovanni M Dall'Olio
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8 days ago,
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For A: Why You Need Perl/Python If You Know R/Shell [Ngs Data Analysis]
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For What Is Your Experience With The String (Interactions) Database?
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For A: Looking For People That Would Try A Custom Genome Viewer That I Wrote For Bioinf
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For C: Computing Number Of Nucleotide And Genes On Each Chromosome
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5 months ago,
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Teacher
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For A: What Is The Input Format For Rnaplot In The Vienna Package?
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7 months ago,
created an answer with at least 3 up-votes.
For A: What Is The Input Format For Rnaplot In The Vienna Package?
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7 months ago,
created a post with more than 5 votes.
For C: Computing Number Of Nucleotide And Genes On Each Chromosome
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7 months ago,
created an answer that was upvoted at least 5 times.
For A: Working with GTEX dataset
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7 months ago,
created an answer with at least 3 up-votes.
For A: What Is The Input Format For Rnaplot In The Vienna Package?
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9 months ago,
created a question with more than 1,000 views.
For Computational Biologist at GSK (Stevenage, UK - between London and Cambridge)
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created a post with more than 5 votes.
For What Is Your Experience With The String (Interactions) Database?
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created a post with more than 5 votes.
For C: Computing Number Of Nucleotide And Genes On Each Chromosome
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For C: Computing Number Of Nucleotide And Genes On Each Chromosome
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10 months ago,
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For A Database Of Signatures Of Selection In The 1000 Genomes Dataset
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10 months ago,
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11 months ago,
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For A Database Of Signatures Of Selection In The 1000 Genomes Dataset
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11 months ago,
created a post with more than 5 votes.
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11 months ago,
created a post with more than 5 votes.
For What Is Your Experience With The String (Interactions) Database?
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12 months ago,
created a question with more than 5,000 views.
For A Database Of Signatures Of Selection In The 1000 Genomes Dataset
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12 months ago,
created a post with more than 5 votes.
For What Is Your Experience With The String (Interactions) Database?
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13 months ago,
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For What Is Your Experience With The String (Interactions) Database?
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