User: svlachavas
svlachavas • 610
- Reputation:
- 610
- Status:
- Trusted
- Location:
- Greece/Athens/National Hellenic Research Foundation
- Last seen:
- 4 days, 2 hours ago
- Joined:
- 3 years, 8 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 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 5 days ago by
svlachavas • 610
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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 6 days ago by
svlachavas • 610
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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 7 days ago by
svlachavas • 610
• updated 6 days ago by
Gordon Smyth ♦ 35k
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... Please, try to answer in English with a complete reply, i did not understand anything from your above answer !!
...
written 7 days ago by
svlachavas • 610
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... Hi mzcs.csu,
have a detailed check on the following posts, they would be very helpful:
https://support.bioconductor.org/p/94554/#94559
https://support.bioconductor.org/p/112949/#112967
Also, a reproducible code chunk with the exact steps you performed would be very helpful-
Best,
Efstathios
...
written 7 days ago by
svlachavas • 610
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... Dear Herve,
thank you for your updated comments and please excuse me for any misunderstanding, as i thought initially that the version of gencode, includes except these sequences that you mentioned above, some extra sequence information about scaffolds, etc-indeed i initially asked the authors abou ...
written 4 weeks ago by
svlachavas • 610
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... Dear Herve,
thank you very much for your answer and comments !! in order to verify that i fully understood your notion:
1) When you mentioned the GRCh38.p12 reference genome, you meant the relative for the gencode reference genome version that i have utilized, correct ? Thus, you believe that even ...
written 4 weeks ago by
svlachavas • 610
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... Dear Community,
based on the analysis results of an exome sequencing project (3 patients with paired cancer and normal samples-Small Cell Lung Cancer-Genomic DNA captured using Agilent in-solution enrichment methodology/paired-end 75 bases massively parallel sequencing on Illumina HiSeq4000)-
both ...
written 4 weeks ago by
svlachavas • 610
• updated 4 weeks ago by
Hervé Pagès ♦♦ 13k
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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 10 weeks 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 10 weeks ago by
svlachavas • 610
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