User: svlachavas

gravatar for svlachavas
svlachavas570
Reputation:
570
Status:
Trusted
Location:
Greece/Athens/National Hellenic Research Foundation
Last seen:
1 day, 20 hours ago
Joined:
2 years, 10 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 • 428 results • page 1 of 43 • next >
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Comment: C: Error and weird result of TCGAanalyze_Normalization function using the R package
... Thanks Davide. I will take a detailed look and perhaps write back or on a different thread for possible related questions. ...
written 2 days ago by svlachavas570
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Comment: C: Error and weird result of TCGAanalyze_Normalization function using the R package
... Dear davide, thank you for your updated answer. Firstly, concerning the geneInfo object head(geneInfo)           geneLength gcContent           chr     100130426 NA         NA                  ""      100133144 "2420"     "0.490495867768595" "chr15" 100134869 "3190"     "0.428526645768025" "chr15 ...
written 2 days ago by svlachavas570
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Comment: C: Error and weird result of TCGAanalyze_Normalization function using the R package
... Dear Davide, thank you for your responce and consideration on this matter !! Firstly, based on your question, the geneInfo argument above, has 2 options to consider: xx <- TCGAbiolinks::geneInfo > head(xx)           geneLength gcContent           chr     100130426 NA         NA              ...
written 3 days ago by svlachavas570
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Error and weird result of TCGAanalyze_Normalization function using the R package TCGAbiolinks for normalization of raw HTSeq counts
... Dear BioCommunity, i recently implemented the R package TCGAbiolinks, to download raw HTSEQ counts for a provinsional cancer TCGA dataset (COAD). My code used was the following: query.exp.hg38 <- GDCquery(project = "TCGA-COAD",  data.category = "Transcriptome Profiling",  data.type = "Gene Expr ...
rnaseq normalization edaseq tcgabiolinks written 5 days ago by svlachavas570 • updated 3 days ago by davide risso520
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Answer: A: Gene level analysis of Affymetrix GeneChip Mouse Exon Arrays
... Dear Gordon, you might find the following paper interesting (https://f1000research.com/articles/5-1384/v1) -it mentions in the abstract that "This workflow is directly applicable to current “Gene” type arrays, e.g. the HuGene or MoGene arrays but can easily adapted to similar platforms..", so it mi ...
written 4 months ago by svlachavas570
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Comment: C: pathway / net-work base analysis with somatic mutations
... AIthough your question of interest is not directed to the purposes of this group, i think MAFFINN tool (http://www.inetbio.org/muffinn/) probably is a valid option for your goal. Best, Efstathios ...
written 5 months ago by svlachavas570
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Answer: A: Alternative packages to limma for analysis of microarray datasets
... Dear Max, personally i would not consider anything better than limma for the analysis of microarray data (not only-)-this has been proven in numerous scientific published papers and pipelines-rather than your approach of using alternative R packages, you could focus on the interpretation of your DE ...
written 6 months ago by svlachavas570
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Dear ghk, perhaps for your need and kind of analysis, you should alternatively try the R package TCGAbiolinks In the link below https://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/query.html you can check from the GDC projects, that there is a one called TCGA-LIHC-so yo ...
written 6 months ago by svlachavas570
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Possible confounding of variable of interest with batch covariate and Partial NA coefficients when including batch in limma linear model for microarray data
... Based on a recent previous post regarding putative batch effect consideration and possible correction for downstream analysis (https://support.bioconductor.org/p/95430/), i show a specific part of my code regarding a statistical downstream analysis with limma in R, for an affymetrix microarray (afte ...
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Answer: A: RNA seq data
... Dear Richa, from your description, one nice package is the TCGAbiolinks R package: https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html You could simply find the specific TCGA cancer projects you wish to analyze, and probably download the HTSeq raw counts-with this format, you co ...
written 6 months ago by svlachavas570

Latest awards to svlachavas

Scholar 6 months ago, created an answer that has been accepted. For A: illuminaHumanv4.db : annotation source, and mapping to transcript names
Popular Question 8 months ago, created a question with more than 1,000 views. For Merge different datasets and perform differential expression analysis in limma
Popular Question 8 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 defining a function for multiple paired t.test in many rows of a microarray dataset
Popular Question 19 months ago, created a question with more than 1,000 views. For Filtering on present/absent calls methodology and perfect match only arrays
Popular Question 19 months ago, created a question with more than 1,000 views. For Use of various distance measures and clustering methods in heatmap creation
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 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 Correct assumptions of using limma moderated t-test
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 20 months ago, created a question with more than 1,000 views. For Error in PCA analysis and with ggbiplot function
Scholar 2.1 years ago, created an answer that has been accepted. For A: illuminaHumanv4.db : annotation source, and mapping to transcript names
Voter 2.1 years ago, voted more than 100 times.
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: MAS 5 package
Scholar 2.4 years ago, created an answer that has been accepted. For A: MAS 5 package
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: MAS 5 package
Scholar 2.4 years ago, created an answer that has been accepted. For A: MAS 5 package

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