User: svlachavas
svlachavas • 640
- Reputation:
- 640
- Status:
- Trusted
- Location:
- Greece/Athens/National Hellenic Research Foundation
- Last seen:
- 6 days, 21 hours ago
- Joined:
- 4 years, 2 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 James, please excuse me for any unintended misunderstanding- indeed these are the relative CEL files for the experiment-i just meant that any information about the experiment, is on an extra excel file, that only mentions the above information- ...
written 7 days ago by
svlachavas • 640
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... Dear James,
thanks for your reply-unfortunately, i have just an excel file-which has an extra description for these cel files with the abbreviation "Clariom_SUM159"-where SUM159 is a cancer cell line-and i can't currently have any other extra information-
thus, you believe that perhaps these are n ...
written 7 days ago by
svlachavas • 640
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... Dear Community,
i have tried recently to read, process and analyze some human clariom array CEL files in R-unfortunately, i have no information from my collaborators which specific platform has been used (for example S or D)-so i tried the following approach:
```
library(oligo)
library(affycoreto ...
written 7 days ago by
svlachavas • 640
• updated
7 days ago by
James W. MacDonald ♦ 49k
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... Dear James, thanks again for bringing up this point. Indeed, my main notion was to take into account some different ideas/suggestions on this matter, and of course then implement my analysis. ...
written 7 weeks ago by
svlachavas • 640
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... Thank you Peter both for your explanations and clarifications !! Regarding your suggestion on "I'd run limma on each cell line separately, then create scatterplots of the fold changes (coefficients) and t statistics" :
you meant, from the raw data-"from scratch" run each batch separately and relati ...
written 7 weeks ago by
svlachavas • 640
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... Thank you Ryan for your considerations on this matter !! indeed, my next actions are to check further componentns/dimensions, as also to test with removeBatchEffect to test the relative changes after-and perhaps i will provide feedback afterwards-
concerning the genas function-as i have never used ...
written 7 weeks ago by
svlachavas • 640
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... Dear James,
thank you for your comment-in fact, I'm fully aware of the tradeoffs and putative solutions-however, even that i have analyzed similar data in the past, i had never encountered thus far this scenario with such a high batch effect presense-that is why, i also created a post here, as much ...
written 7 weeks ago by
svlachavas • 640
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... Dear Community,
I'm currently try to analyze one microarray dataset, essentially comprised of 3 different cell lines/batches, each one having the same experimental design: the deletion (CRISPR/Cas9) of a specific gene, and includes WT (wild type) samples, versus knock-out samples. After import, nor ...
written 7 weeks ago by
svlachavas • 640
• updated
7 weeks ago by
Ryan C. Thompson ♦ 7.2k
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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 4 months ago by
svlachavas • 640
• updated
4 months 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 5 months ago by
svlachavas • 640
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