User: svlachavas

gravatar for svlachavas
svlachavas610
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

<prev • 466 results • page 1 of 47 • next >
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Comment: C: How to analyze correctly agilent two-colour microarray data from the ArrayExpres
... 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 svlachavas610
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Comment: C: How to analyze correctly agilent two-colour microarray data from the ArrayExpres
... 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 svlachavas610
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How to analyze correctly agilent two-colour microarray data from the ArrayExpress repository with the limma R package
... 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 ...
limma arrayexpress agilent microarrays nchannelset written 7 days ago by svlachavas610 • updated 6 days ago by Gordon Smyth35k
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Comment: C: Help for Affymetrix HTA 2.0 [transcript (gene) version] annotation
... Please, try to answer in English with a complete reply, i did not understand anything from your above answer !! ...
written 7 days ago by svlachavas610
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Answer: A: Help for Affymetrix HTA 2.0 [transcript (gene) version] annotation
... 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 svlachavas610
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Comment: C: Include and implement a new reference genome option in the R package BSgenome fo
... 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 svlachavas610
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Comment: C: Include and implement a new reference genome option in the R package BSgenome fo
... 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 svlachavas610
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Include and implement a new reference genome option in the R package BSgenome for downstream variant calling analysis
... 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 ...
bsgenome reference genome gencode whole exome sequence variant calling written 4 weeks ago by svlachavas610 • updated 4 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: Implementation of specific cpm filtering in RNA-Seq data described in a previous
... 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 svlachavas610
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Comment: C: Implementation of specific cpm filtering in RNA-Seq data described in a previous
... 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 svlachavas610

Latest awards to svlachavas

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Problem with the colors in the heatmap.2 function and the color key values range
Popular Question 4 months ago, created a question with more than 1,000 views. For Questions in limma about multifactorial design and possible batch effect correction
Popular Question 15 months ago, created a question with more than 1,000 views. For Important r packages not available for R version 3.1.1
Popular Question 15 months ago, created a question with more than 1,000 views. For Problems importing Illumina raw data with lumi R package
Popular Question 15 months ago, created a question with more than 1,000 views. For Update R in Rstudio to specific version 3.2.1 in windows
Popular Question 15 months ago, created a question with more than 1,000 views. For Questions in limma about multifactorial design and possible batch effect correction
Popular Question 15 months ago, created a question with more than 1,000 views. For Correct assumptions of using limma moderated t-test
Popular Question 15 months ago, created a question with more than 1,000 views. For (Gene-set)Pathway analysis based on network/pathway topology in R
Student 15 months ago, asked a question with at least 3 up-votes. For Appropriate use of the function treat of the limma package
Popular Question 15 months ago, created a question with more than 1,000 views. For Error in PCA analysis and with ggbiplot function
Scholar 16 months ago, created an answer that has been accepted. For A: illuminaHumanv4.db : annotation source, and mapping to transcript names
Popular Question 18 months ago, created a question with more than 1,000 views. For Merge different datasets and perform differential expression analysis in limma
Popular Question 18 months ago, created a question with more than 1,000 views. For Update R in Rstudio to specific version 3.2.1 in windows

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