Moderator: Giovanni M Dall'Olio

Reputation:
25,790
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Trusted
Location:
London, UK
Website:
http://bioinfoblog.it/
Twitter:
dalloliogm
Scholar ID:
Google Scholar Page
Last seen:
55 minutes ago
Joined:
8 years, 10 months ago
Email:
d*********@gmail.com

Research Associate at the King's College of London. Interested in human population genetics and cancer.

Posts by Giovanni M Dall'Olio

<prev • 1,374 results • page 1 of 138 • next >
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Comment: C: How to interpret XPEHH (recent selection) score?
... 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 8 weeks ago by Giovanni M Dall'Olio26k
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Answer: A: GTEx Analysis V7 RNA-seq dataset download
... 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 9 months ago by Giovanni M Dall'Olio26k
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Answer: C: as.integer function is converting row names in to number
... Explanation: your column is stored as factors Solution1: as.integer(as.character(mycolumn)) Solution2: use stringAsFactors=F when reading the data ...
written 9 months ago by Giovanni M Dall'Olio26k
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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 12 months ago by Giovanni M Dall'Olio26k
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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 16 months ago by Giovanni M Dall'Olio26k
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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 16 months ago by Giovanni M Dall'Olio26k
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Answer: A: Converting gene ids to each other
... 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 17 months ago by Giovanni M Dall'Olio26k
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Comment: C: Poll: How many people have PyPy?
... Why would I need to have PyPy installed? ...
written 17 months ago by Giovanni M Dall'Olio26k
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Comment: C: PCA for deregulated genes - technical question
... 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 18 months ago by Giovanni M Dall'Olio26k
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Comment: C: Different results with edgeR when adding gene symbols
... how many rows do you have before and after adding the gene names? ...
written 18 months ago by Giovanni M Dall'Olio26k

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Prophet 4 weeks ago, created a post with more than 20 followers. For A Database Of Signatures Of Selection In The 1000 Genomes Dataset
Teacher 6 weeks 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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Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Looking For People That Would Try A Custom Genome Viewer That I Wrote For Bioinf
Appreciated 5 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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Good Question 7 months ago, asked a question that was upvoted at least 5 times. For What Is Your Experience With The String (Interactions) Database?
Teacher 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?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: What Is The Input Format For Rnaplot In The Vienna Package?
Appreciated 9 months ago, created a post with more than 5 votes. For C: Computing Number Of Nucleotide And Genes On Each Chromosome
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Working with GTEX dataset
Teacher 9 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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Appreciated 11 months ago, created a post with more than 5 votes. For What Is Your Experience With The String (Interactions) Database?
Appreciated 11 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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Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Computing Number Of Nucleotide And Genes On Each Chromosome
Great Question 12 months ago, created a question with more than 5,000 views. For A Database Of Signatures Of Selection In The 1000 Genomes Dataset
Appreciated 13 months ago, created a post with more than 5 votes. For What Is Your Experience With The String (Interactions) Database?
Appreciated 13 months ago, created a post with more than 5 votes. For What Is Your Experience With The String (Interactions) Database?
Great Question 14 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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