User: svlachavas

gravatar for svlachavas
svlachavas640
Reputation:
640
Status:
Trusted
Location:
Greece/Athens/National Hellenic Research Foundation
Last seen:
6 days, 21 hours ago
Joined:
4 years, 2 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 • 480 results • page 1 of 48 • next >
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Comment: C: Correct annotation R package for human clariom array analysis
... Dear James, please excuse me for any unintended misunderstanding- indeed these are the relative CEL files for the experiment-i just meant that any information about the experiment, is on an extra excel file, that only mentions the above information- ...
written 7 days ago by svlachavas640
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Comment: C: Correct annotation R package for human clariom array analysis
... Dear James, thanks for your reply-unfortunately, i have just an excel file-which has an extra description for these cel files with the abbreviation "Clariom_SUM159"-where SUM159 is a cancer cell line-and i can't currently have any other extra information- thus, you believe that perhaps these are n ...
written 7 days ago by svlachavas640
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Correct annotation R package for human clariom array analysis
... Dear Community, i have tried recently to read, process and analyze some human clariom array CEL files in R-unfortunately, i have no information from my collaborators which specific platform has been used (for example S or D)-so i tried the following approach: ``` library(oligo) library(affycoreto ...
affycoretools oligo pd.hugene.2.0.st clariom written 7 days ago by svlachavas640 • updated 7 days ago by James W. MacDonald49k
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Comment: C: Taking into account strong batch effect in microarray differential expression an
... Dear James, thanks again for bringing up this point. Indeed, my main notion was to take into account some different ideas/suggestions on this matter, and of course then implement my analysis. ...
written 7 weeks ago by svlachavas640
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Comment: C: Taking into account strong batch effect in microarray differential expression an
... Thank you Peter both for your explanations and clarifications !! Regarding your suggestion on "I'd run limma on each cell line separately, then create scatterplots of the fold changes (coefficients) and t statistics" : you meant, from the raw data-"from scratch" run each batch separately and relati ...
written 7 weeks ago by svlachavas640
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Comment: C: Taking into account strong batch effect in microarray differential expression an
... Thank you Ryan for your considerations on this matter !! indeed, my next actions are to check further componentns/dimensions, as also to test with removeBatchEffect to test the relative changes after-and perhaps i will provide feedback afterwards- concerning the genas function-as i have never used ...
written 7 weeks ago by svlachavas640
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Comment: C: Taking into account strong batch effect in microarray differential expression an
... Dear James, thank you for your comment-in fact, I'm fully aware of the tradeoffs and putative solutions-however, even that i have analyzed similar data in the past, i had never encountered thus far this scenario with such a high batch effect presense-that is why, i also created a post here, as much ...
written 7 weeks ago by svlachavas640
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Taking into account strong batch effect in microarray differential expression analysis with limma
... Dear Community, I'm currently try to analyze one microarray dataset, essentially comprised of 3 different cell lines/batches, each one having the same experimental design: the deletion (CRISPR/Cas9) of a specific gene, and includes WT (wild type) samples, versus knock-out samples. After import, nor ...
microarray limma batch effect de hugenest written 7 weeks ago by svlachavas640 • updated 7 weeks ago by Ryan C. Thompson7.2k
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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 4 months ago by svlachavas640 • updated 4 months 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 5 months ago by svlachavas640

Latest awards to svlachavas

Student 3 months ago, asked a question with at least 3 up-votes. For Appropriate use of the function treat of the limma package
Popular Question 4 months ago, created a question with more than 1,000 views. For Background correction in Illumina beadchip microarrays with limma neqc function
Popular Question 5 months ago, created a question with more than 1,000 views. For Correct assumptions of using limma moderated t-test
Popular Question 5 months ago, created a question with more than 1,000 views. For Error in PCA analysis and with ggbiplot function
Popular Question 7 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 10 months ago, created a question with more than 1,000 views. For Questions in limma about multifactorial design and possible batch effect correction
Student 21 months ago, asked a question with at least 3 up-votes. For Appropriate use of the function treat of the limma package
Popular Question 21 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 21 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 21 months ago, created a question with more than 1,000 views. For Error in PCA analysis and with ggbiplot function
Popular Question 21 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 21 months ago, created a question with more than 1,000 views. For Problems importing Illumina raw data with lumi R package
Popular Question 21 months ago, created a question with more than 1,000 views. For Correct assumptions of using limma moderated t-test

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