User: svlachavas

gravatar for svlachavas
svlachavas630
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

<prev • 472 results • page 1 of 48 • next >
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Apply different cutoffs with edgeR pipeline and glmTreat for RNA-Seq DEG analysis
... 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 ...
edger differential gene expression glmtreat written 12 weeks ago by svlachavas630 • updated 11 weeks ago by Gordon Smyth36k
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Comment: C: Explanation of mroast results for specific biological processes and error with b
... 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 svlachavas630
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Explanation of mroast results for specific biological processes and error with barcodeplot function with a microarray dataset
... 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] ...
limma mroast barcodeplot agilent microarrays go.bp written 3 months ago by svlachavas630 • updated 3 months ago by Gordon Smyth36k
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Comment: C: Perform limma based gene-set testing for a two-group comparison in a microarray
... 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 svlachavas630
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Comment: C: Perform limma based gene-set testing for a two-group comparison in a microarray
... 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 svlachavas630
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Perform limma based gene-set testing for a two-group comparison in a microarray dataset regarding specific biological processes
... 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 ...
limma mroast gene set testing agilent microarrays fry gene tests written 3 months ago by svlachavas630 • updated 3 months ago by Gordon Smyth36k
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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 4 months ago by svlachavas630
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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 4 months ago by svlachavas630
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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 4 months ago by svlachavas630 • updated 4 months ago by Gordon Smyth36k
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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 4 months ago by svlachavas630

Latest awards to svlachavas

Student 8 weeks ago, asked a question with at least 3 up-votes. For Appropriate use of the function treat of the limma package
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Background correction in Illumina beadchip microarrays with limma neqc function
Popular Question 3 months ago, created a question with more than 1,000 views. For Correct assumptions of using limma moderated t-test
Popular Question 3 months ago, created a question with more than 1,000 views. For Error in PCA analysis and with ggbiplot function
Popular Question 5 months 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 8 months ago, created a question with more than 1,000 views. For Questions in limma about multifactorial design and possible batch effect correction
Student 19 months ago, asked a question with at least 3 up-votes. For Appropriate use of the function treat of the limma package
Popular Question 19 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 19 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 19 months ago, created a question with more than 1,000 views. For Error in PCA analysis and with ggbiplot function
Popular Question 19 months ago, created a question with more than 1,000 views. For (Gene-set)Pathway analysis based on network/pathway topology in R
Popular Question 19 months ago, created a question with more than 1,000 views. For Problems importing Illumina raw data with lumi R package
Popular Question 19 months ago, created a question with more than 1,000 views. For Correct assumptions of using limma moderated t-test

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