User: svlachavas
svlachavas • 740
- Reputation:
- 740
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- Location:
- Greece/Athens/National Hellenic Research Foundation
- Last seen:
- 2 weeks, 3 days ago
- Joined:
- 4 years, 9 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 KCLiv,
if i have understood correctly you have "normalized estimated counts from RSEM" - i have faced previously a similar situation and you can check one of my previous posts with suggested solutions-briefly:
https://support.bioconductor.org/p/91054/#95981
1) Continue with the limma-trend p ...
written 19 days ago by
svlachavas • 740
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... Dear li.zhaoz,
it is important before to proceed to read the following posts/articles about rna-seq analysis, normalization and transformation methodologies:
https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/
https://academic.oup.com/bib/article/14/6/6 ...
written 19 days ago by
svlachavas • 740
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... Dear Anita,
even your question is not directly related to the purpose of this group, i would quickly suggest for a solution through R/Bioconductor
the R package CoRegNet [http://bioconductor.org/packages/release/bioc/html/CoRegNet.html]-but the relative gene expression data are necessary for the c ...
written 27 days ago by
svlachavas • 740
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... Thank you one more time Levi for the feedback and information-i fully understand that the nature and type of normalization is upon me and how i should proceed-the workshop link looks great, so i think that based on your functions and tutorials, subsetting and moving for downstream analysis will not ...
written 6 months ago by
svlachavas • 740
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... Dear Levi,
thank you very much for your detailed answer, suggestions and putative steps-some crusial comments:
1) The link above that you have included does not work- so it is possible to search or check which processing steps with which algorithms the assays **"miRNASeqGene"** and **"RNASeq2Gene ...
written 6 months ago by
svlachavas • 740
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Dear Community,
briefly, based on a previously identified gene signature in a specific type of cancer (through gene expression analysis), in parallel i found also 4 specific microRNAs (mature miRs) that regulate a specific subset of my signature (~18 genes) via experimentally validated databases. ...
written 6 months ago by
svlachavas • 740
• updated
6 months ago by
Levi Waldron ♦ 950
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Dear Community,
I’m currently analyzing an RNA-Seq gene expression dataset, downloaded from the recount project. It includes trios of paired samples of primary cancers, their liver metastases and their normal adjucent tissue samples (18 patients-54 samples). The code chunk used for downstream anal ...
written 6 months ago by
svlachavas • 740
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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 months ago by
svlachavas • 740
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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 months ago by
svlachavas • 740
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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 months ago by
svlachavas • 740
• updated
7 months ago by
James W. MacDonald ♦ 51k
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