User: sjorsvanheuveln

Reputation:
50
Status:
New User
Location:
Netherlands
Last seen:
3 years, 6 months ago
Joined:
4 years, 2 months ago
Email:
s**************@gmail.com

Bioinformatics master student @ Vrije Universiteit Amsterdam (the Netherlands). Currently doing an internship on cisplatin response prediction at the Netherlands Cancer Institute.

 

Posts by sjorsvanheuveln

<prev • 11 results • page 1 of 2 • next >
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Comment: C: How To Associate Cpg Coordinate With The Gene Names Or Entrez Id
... Here's the R-code. source("https://bioconductor.org/biocLite.R") biocLite("IlluminaHumanMethylation450k.db") library(IlluminaHumanMethylation450k.db) CpG_annotation <- as.list(IlluminaHumanMethylation450kSYMBOL[mappedkeys(IlluminaHumanMethylation450kSYMBOL)]) ...
written 3.5 years ago by sjorsvanheuveln50
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Comment: C: Feature Selection method dependent on response variable?
... Thanks Steven, What if I don't want to discretize my response variable into groups? In that case it would definitely influence feature selection techniques applicable to this problem, right? I'm currently reading [this][1] article by Hira & Gillies (2015), which makes distinctions between FS te ...
written 3.5 years ago by sjorsvanheuveln50
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Comment: C: Latest Regression techniques for Microarray data
... Actually, isn't a random survival forest only just suited for predicting time of survival of a population. Can it be transferred to age prediction, which seems to be something else? ...
written 3.6 years ago by sjorsvanheuveln50
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Comment: C: Latest Regression techniques for Microarray data
... Yeah nice idea. Seems to be an interesting candidate. And it has also got an R-package, so that's awesome too. ...
written 3.6 years ago by sjorsvanheuveln50
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Feature Selection method dependent on response variable?
... I have a 450k Inifinium DNA methylation microarray data and I want to predict age (continuous response variable) from this data. As there are way more features than samples, I will have to apply feature selection. I was wondering, is my choice of feature selection partially determined by the type of ...
data modeling feature selection microarray written 3.6 years ago by sjorsvanheuveln50 • updated 3.6 years ago by Steven Lakin1.4k
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Latest Regression techniques for Microarray data
... I'm currently studying which models would best work in predicting age (continuous variable) from DNA-methylation microarrays. As, nowadays there are many extensions/variations becoming available based on (penalized) regression techniques, I was wondering which techniques are now out there that can b ...
R modeling microarray regression written 3.6 years ago by sjorsvanheuveln50
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Where can I find a list of driver mutations in Triple Negative Breast Cancer?
... Where can I download a list of known and confirmed driver mutations in Triple Negative Breast Cancer? ...
tnbc driver mutation breast cancer written 3.9 years ago by sjorsvanheuveln50
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Answer: A: Probability Of Gene List Overlap
... If you want to know what the chance is for exactly q+1 number of overlapping genes, you should subtract the the phyper function like this: phyper(q, m, n, k, lower.tail = F) - phyper(q+1, m, n, k, lower.tail = F) (with q the number of overlaps -1) This is because phyper gives the chance for q+1 ...
written 4.1 years ago by sjorsvanheuveln50
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Comment: C: How to convert segmented aCGH probe-based to gene-based?
... Thanks a million Arno, this worked for me!  ...
written 4.1 years ago by sjorsvanheuveln50
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How to convert segmented aCGH probe-based to gene-based?
... I'm looking for the easiest method in R to convert my segmented aCGH probes into log ratios per gene (they're not called). Furthermore I only have chromosome number and start position available. What is the best way to achieve this goal?   ...
gene acgh probe conversion R written 4.1 years ago by sjorsvanheuveln50 • updated 3.1 years ago by Biostar ♦♦ 20

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