User: svlachavas
svlachavas • 630
- Reputation:
- 630
- Status:
- Trusted
- Location:
- Greece/Athens/National Hellenic Research Foundation
- Last seen:
- 14 hours ago
- Joined:
- 4 years 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 Bioconductor community,
based on a recent analysis of an RNA-Seq gene expression analysis concerning different cancer cell lines, i was trying to apply the relative Treat methodology for various biological contrasts of interest, in order to narrow my DEGlists, as significant differences have ...
written 12 weeks ago by
svlachavas • 630
• updated
11 weeks ago by
Gordon Smyth ♦ 36k
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... Dear Gordon,
thank you for your clarification, especially on the first 2 questions. If i could re-formulate my initial questions more appropriatelly, my main goal/concern, if with the aim of significance, i could choose the mixed Pvalues-for these specific terms-instead of the one direction Pvalues ...
written 3 months ago by
svlachavas • 630
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... Dear Community, based on a description on a previous post (https://support.bioconductor.org/p/113809/#113950) i tried to implement mroast gene set testing in limma with specific Gene Ontology Biological Processes:
# my expression microarray dataset:
class(final)
[1] "EList"
attr(,"package")
[1] ...
written 3 months ago by
svlachavas • 630
• updated
3 months ago by
Gordon Smyth ♦ 36k
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... Dear Gordon, thank you for your updates for my first question part-however, I'm facing a specific downstream issue:
Symbols <- rownames(final)
dat <- alias2SymbolUsingNCBI(Symbols, "Homo_sapiens.gene_info")
head(dat)
GeneID Symbol description
14710 ...
written 3 months ago by
svlachavas • 630
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... Dear Gordon, thank you very much for the very useful comment-i have used in the past-based also on your suggestion-alias2SymbolTable, but i haven't checked that alias2SymbolUsingNCBI() returns also GeneIDs-
moreover, regarding my initial question, concerning the type of gene set ? you would choose ...
written 3 months ago by
svlachavas • 630
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... Dear Community,
based on some initial in vitro experiments, and a subsequent cancer microarray dataset analysis in R, i would like to perform some gene-set tests, for specific pathways and ontologies, regarding my phenotype of interest. Briefly, based on a two-group condition, we are mostly interes ...
written 3 months ago by
svlachavas • 630
• updated
3 months ago by
Gordon Smyth ♦ 36k
0
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... Dear Gordon, thank you for your valuable comments and considerations-without the intention to disturb you more, i will just add some quick final comments based on your suggestions:
1) Firstly, based on your initial part of your answer, you meant something like the following ? based on the "old" ann ...
written 4 months ago by
svlachavas • 630
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... Dear Gordon,
thank you one more time for your feedback-i would like just to add some crusial comments based on my downstream analysis, in which I'm facing some issues :
Initially, based on your suggestion, i downloaded the 3 zipped parts of the dataset, unzipped them, and then use the SDRF file of ...
written 4 months ago by
svlachavas • 630
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... Dear Community,
for an ongoing collaborative project, i want to analyze a transcriptomic dataset, which is not deposited in GEO, but in ArrayExpress:
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6326/?page=1&pagesize=500
So, through the R package arrayexpress, i tried initially to do ...
written 4 months ago by
svlachavas • 630
• updated
4 months ago by
Gordon Smyth ♦ 36k
0
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... Please, try to answer in English with a complete reply, i did not understand anything from your above answer !!
...
written 4 months ago by
svlachavas • 630
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