User: svlachavas

gravatar for svlachavas
svlachavas • 530
Reputation:
530
Status:
Trusted
Location:
Greece/Athens/National Hellenic Research Foundation
Last seen:
4 hours ago
Joined:
2 years, 5 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 • 423 results • page 1 of 43 • next >
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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 21 days ago by svlachavas • 530
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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 5 weeks ago by svlachavas • 530
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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 5 weeks ago by svlachavas • 530
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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 ...
microarray limma batch effect design matrix confounding written 7 weeks ago by svlachavas • 530
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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 7 weeks ago by svlachavas • 530
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Answer: A: fdr score for degs
... Dear Nia, your question if using a specific fdr cutoff is very general, and has not a specific answer-using a specific FDR cutoff-lets say 0.05- is generally arbitary-conventional and mostly there is no "consensus" about the "best fdr", as it simply depends mostly on what conclusions you want to dr ...
written 7 weeks ago by svlachavas • 530
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Answer: A: Meaning of multiple coef in topTable, limma.
... Dear Zhang, when you define multiple coefficients (or no coefficients set), you actually perform an ANOVA-like comparison (similarly if you instead use topTableF), where your null hypothesis would be that there are no DE between any of the conditions/defined coefficients. Thus, in the first case wh ...
written 7 weeks ago by svlachavas • 530
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Answer: A: Search for Drugs related to results of differential expression analysis using RN
... Dear bioinformatics,  actually i think this a rather off-topic post, as it is not "mandatory" to use any Bioconductor/R packages related to your question of interest. Actually, i would argue why you would like to use R for this kind of analysis ? considering only the gene expression list from the R ...
written 7 weeks ago by svlachavas • 530
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Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
... Dear Community, i'm currently analyzing a dataset of human HTA 2.0 affymetrix microarrays, for statistical analysis of a two-group comparison (healthy subjects and different subject samples from a autoimmune chronic disease). After import/pre-processing/normalization, i created further some EDA pl ...
limma combat batch effect affymetrix microarrays hta2.0 written 7 weeks ago by svlachavas • 530
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Comment: C: Problem with GEOquery R package in Windows when trying to download specific GEO
... Dear Sean, thank you for your comprehensive answer !! i usually download raw files, but this time due to the very large size of the raw data, i saw "naively" from this link (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE88884) the abbreviation GSE88884_ILLUMINATE1and2_SLEbaselineVsHealthy_p ...
written 10 weeks ago by svlachavas • 530

Latest awards to svlachavas

Popular Question 6 weeks ago, created a question with more than 1,000 views. For GeneChip Human Transcriptome Array 2.0 analysis in R for identifying possible differential exon splicing events
Scholar 7 weeks ago, created an answer that has been accepted. For A: illuminaHumanv4.db : annotation source, and mapping to transcript names
Popular Question 3 months ago, created a question with more than 1,000 views. For Merge different datasets and perform differential expression analysis in limma
Popular Question 3 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 3 months ago, created a question with more than 1,000 views. For Error and questions about clustering & ploting functions in r packages cluster and mclust regarding kmeans method
Popular Question 3 months ago, created a question with more than 1,000 views. For Error and questions about clustering & ploting functions in r packages cluster and mclust regarding kmeans method
Popular Question 14 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 14 months ago, created a question with more than 1,000 views. For Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
Popular Question 14 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 14 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 14 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 14 months ago, created a question with more than 1,000 views. For Appropriate use of the function treat of the limma package
Popular Question 14 months ago, created a question with more than 1,000 views. For Error using function NbClust regarding multiple values in the argument "index" of package NbClust for getting the optimal number of clusters of a dataset
Popular Question 14 months ago, created a question with more than 1,000 views. For "Error in readRDS(file) : unknown input format" appearing every time starting Rstudio after BiocUpgrade
Popular Question 14 months ago, created a question with more than 1,000 views. For Correct assumptions of using limma moderated t-test
Popular Question 14 months ago, created a question with more than 1,000 views. For GeneChip Human Transcriptome Array 2.0 analysis in R for identifying possible differential exon splicing events
Popular Question 14 months ago, created a question with more than 1,000 views. For Error in PCA analysis and with ggbiplot function
Popular Question 14 months ago, created a question with more than 1,000 views. For Error and questions about clustering & ploting functions in r packages cluster and mclust regarding kmeans method
Popular Question 15 months ago, created a question with more than 1,000 views. For Error in PCA analysis and with ggbiplot function
Scholar 20 months ago, created an answer that has been accepted. For A: illuminaHumanv4.db : annotation source, and mapping to transcript names
Voter 20 months ago, voted more than 100 times.
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: MAS 5 package
Scholar 23 months ago, created an answer that has been accepted. For A: MAS 5 package
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: MAS 5 package
Scholar 24 months ago, created an answer that has been accepted. For A: MAS 5 package
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