User: svlachavas

gravatar for svlachavas
svlachavas510
Reputation:
510
Status:
Trusted
Location:
Greece/Athens/National Hellenic Research Foundation
Last seen:
2 days, 8 hours ago
Joined:
2 years, 4 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 • 422 results • page 1 of 43 • next >
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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 days ago by svlachavas510
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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 8 days ago by svlachavas510
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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 20 days ago by svlachavas510
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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 20 days ago by svlachavas510
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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 21 days ago by svlachavas510
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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 21 days ago by svlachavas510
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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 ...
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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 6 weeks ago by svlachavas510
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Problem with GEOquery R package in Windows when trying to download specific GEO processed data
... Dear Community, based on the very large size of raw data of a specific affymetrix HTA 2.0 dataset in GEO (with GSE88884), i used the following small code chunk to download the processed data: library(GEOquery) gseList = getGEO("GSE88884") https://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88884/ ...
geoquery windows8 affymetrix microarrays getgeo written 6 weeks ago by svlachavas510 • updated 6 weeks ago by Sean Davis20k

Latest awards to svlachavas

Scholar 19 days ago, created an answer that has been accepted. For A: illuminaHumanv4.db : annotation source, and mapping to transcript names
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Merge different datasets and perform differential expression analysis in limma
Popular Question 9 weeks 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 13 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 13 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 13 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 13 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 13 months ago, created a question with more than 1,000 views. For Appropriate use of the function treat of the limma package
Popular Question 13 months ago, created a question with more than 1,000 views. For Correct assumptions of using limma moderated t-test
Popular Question 13 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 in PCA analysis and with ggbiplot function
Scholar 19 months ago, created an answer that has been accepted. For A: illuminaHumanv4.db : annotation source, and mapping to transcript names
Voter 19 months ago, voted more than 100 times.
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: MAS 5 package
Scholar 22 months ago, created an answer that has been accepted. For A: MAS 5 package
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

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