Moderator: Giovanni M Dall'Olio

Reputation:
25,970
Status:
Trusted
Location:
London, UK
Website:
http://bioinfoblog.it/
Twitter:
dalloliogm
Scholar ID:
Google Scholar Page
Last seen:
4 weeks ago
Joined:
8 years, 12 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 • 1,377 results • page 1 of 138 • next >
0
votes
1
answer
162
views
1
answers
Comment: C: Why use LASSO / elastic net in survival regression?
... What about doing a PCA first, then cox or other regressions on the components? The PCA would deal with correlation among the variables. The lasso regression would penalize correlated variables and possibly remove them from the model (as they will have lower betas), but is that what you really want? ...
written 6 weeks ago by Giovanni M Dall'Olio26k
8
votes
2
answers
5.9k
views
2
answers
Answer: A: PCA in a RNA seq analysis
... (the following is a dramatization of the reality - but is generally true. You can think of it as the legend of the PCA) For many centuries, the scientific community believed in what is written in the bible, which is that **all humans are created equals, and there are no differences between people** ...
written 7 weeks ago by Giovanni M Dall'Olio26k
2
votes
2
answers
5.9k
views
2
answers
Comment: C: PCA in a RNA seq analysis
... If you look at the pairs plots, you will notice that there it seems to be no correlation between any of the components. That in fact is an important property of the components - there is no correlation between them. If you have a dataset containing multiple variables and some of these are correlated ...
written 7 weeks ago by Giovanni M Dall'Olio26k
1
vote
1
answer
3.8k
views
1
answers
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 3 months ago by Giovanni M Dall'Olio26k
1
vote
1
answer
1.4k
views
1
answers
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 11 months ago by Giovanni M Dall'Olio26k
0
votes
1
answer
257
views
1
answers
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 11 months ago by Giovanni M Dall'Olio26k
1
vote
3
answers
2.4k
views
3
answers
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 14 months ago by Giovanni M Dall'Olio26k
1
vote
1
answer
1.1k
views
1
answers
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 18 months ago by Giovanni M Dall'Olio26k
0
votes
1
answer
1.1k
views
1
answers
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 18 months ago by Giovanni M Dall'Olio26k
6
votes
4
answers
933
views
4
answers
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 19 months ago by Giovanni M Dall'Olio26k

Latest awards to Giovanni M Dall'Olio

Scholar 6 weeks ago, created an answer that has been accepted. For A: How TCGA generanker works ?
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: Remove Some Snps In Plink
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Would There Be Interest In A 'Next-Gen Sequencing' Stackexchange Site?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: What Is The Input Format For Rnaplot In The Vienna Package?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: What Is The Input Format For Rnaplot In The Vienna Package?
Prophet 3 months ago, created a post with more than 20 followers. For A Database Of Signatures Of Selection In The 1000 Genomes Dataset
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What Is The Input Format For Rnaplot In The Vienna Package?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Why You Need Perl/Python If You Know R/Shell [Ngs Data Analysis]
Scholar 4 months ago, created an answer that has been accepted. For A: How TCGA generanker works ?
Appreciated 4 months ago, created a post with more than 5 votes. For What Is Your Experience With The String (Interactions) Database?
Scholar 6 months ago, created an answer that has been accepted. For A: How TCGA generanker works ?
Good Answer 7 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 7 months ago, created a post with more than 5 votes. For C: Computing Number Of Nucleotide And Genes On Each Chromosome
Student 9 months ago, asked a question with at least 3 up-votes. For What Is Snp Calling?
Good Question 9 months ago, asked a question that was upvoted at least 5 times. For What Is Your Experience With The String (Interactions) Database?
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?
Teacher 11 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 11 months ago, created a post with more than 5 votes. For C: Computing Number Of Nucleotide And Genes On Each Chromosome
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Working with GTEX dataset
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: What Is The Input Format For Rnaplot In The Vienna Package?
Popular Question 13 months ago, created a question with more than 1,000 views. For Computational Biologist at GSK (Stevenage, UK - between London and Cambridge)
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 C: Computing Number Of Nucleotide And Genes On Each Chromosome
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Computing Number Of Nucleotide And Genes On Each Chromosome
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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1131 users visited in the last hour