User: svlachavas
svlachavas • 610
- Reputation:
- 610
- Status:
- Trusted
- Location:
- Greece/Athens/National Hellenic Research Foundation
- Last seen:
- 1 day, 2 hours ago
- Joined:
- 3 years, 6 months ago
- Email:
- s*********@eie.gr
I'm currently working as a PhD candidate at National Hellenic Research Foundation under the team of Metabolic Engineering & Bioinformatics, in Greece (http://www.eie.gr/nhrf/institutes/ibrb/programmes/metabolicengineering-en.html). My BSc Degree is in Molecular Biology and Genetics and my MSc Degree in Master’s Degree Program of Clinical Pharmacology and Therapeutics-Organized by the Medical School of the Democritus University of Thrace in collaboration with The Medical School of the University of Crete. My main interests focus on the development of computational & molecular methodologies empowering translational biomedical cancer research.
Posts by svlachavas
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... Dear Gordon,
thank you for your answer and clarifications-just a small comment, that i would like your opinion-despite not doing an edgeR DE analysis, you would agree that still filtering, even for using only the gene signature in downstream analysis, would still be initially beneficial for TMM nor ...
written 5 days ago by
svlachavas • 610
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... Dear James, thank you for your suggestion-and I'm aware of the above function-however, as i have described in my previous link post, as i include only cancer samples, in the start there are not any pre-defined groups-only after downstream clustering, etc-thus, this function is not convinient in my p ...
written 5 days ago by
svlachavas • 610
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... Dear Community,
i would like to ask a specific question concering a published paper with title : "It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR" (https://link.springer.com/protocol/10.1007%2F978-1-4939-3578-9_19) and th ...
written 6 days ago by
svlachavas • 610
• updated 5 days ago by
Gordon Smyth ♦ 34k
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... Ok Aaron gotcha
...
written 6 days ago by
svlachavas • 610
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... Dear Aaron,
sorry to return again on this post, but i would like to add a very important question concering a published paper in which you are the author with title : "It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR" (htt ...
written 6 days ago by
svlachavas • 610
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... Dear Valerie,
thank you for your consideration on this matter-i have created also a post in the github account, but still i have not received an answer, as also from previous emails to the authors i did not get an answer, so i do not know if things are active-any custom solution you would support ? ...
written 10 days ago by
svlachavas • 610
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... Dear Valerie, sorry to return again but this time, a new error appeared using the same exact code:
snps.vcf <- snps.from.file(file=vcf_files,search.genome =BSgenome.Hsapiens.UCSC.hg38,format = "vcf")
Error in info(snps) : could not find function "info"
In addition: Warning message:
In .bcfHeade ...
written 11 days ago by
svlachavas • 610
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... Dear Mario,
have you checked the tutorial of the MultiAssayExperiment R package:
https://bioconductor.org/packages/release/bioc/vignettes/MultiAssayExperiment/inst/doc/QuickStartMultiAssay.html
as also the quick cheatsheet arguments and functions:
https://bioconductor.org/packages/release/bioc ...
written 21 days ago by
svlachavas • 610
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... Thank you Marcel for your updated answer-just an extra point that i forgot to mention for my answer-concering the data the MultiAssayExperiment containts, they are indeed hg19 correct ? And for the cox hazard model, if i find the same subset of genes with the hg19 analysis, significantly related wit ...
written 22 days ago by
svlachavas • 610
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... Dear Marcel,
thank you for your quick comments and suggestions-just to recap and summarize some important comments based on your answer:
1) Yes, I'm a frequent user of TCGAbiolinks. mainly for analyzing transcriptomic and mutational data. However, for example there are various discrepancies when m ...
written 22 days ago by
svlachavas • 610
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