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Moderator: Giovanni M Dall'Olio

gravatar for Giovanni M Dall'Olio
Reputation:
25,970
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Location:
London, UK
Website:
http://bioinfoblog.it/
Twitter:
dalloliogm
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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

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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'Olio ♦ 26k
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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'Olio ♦ 26k
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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'Olio ♦ 26k
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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 3 months ago by Giovanni M Dall'Olio ♦ 26k
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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 11 months ago by Giovanni M Dall'Olio ♦ 26k
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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 11 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 14 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 18 months ago by Giovanni M Dall'Olio ♦ 26k
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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 18 months ago by Giovanni M Dall'Olio ♦ 26k
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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 19 months ago by Giovanni M Dall'Olio ♦ 26k

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