User: svlachavas

gravatar for svlachavas
svlachavas660
Reputation:
660
Status:
Trusted
Location:
Greece/Athens/National Hellenic Research Foundation
Last seen:
2 months, 3 weeks ago
Joined:
4 years, 6 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 • 484 results • page 1 of 49 • next >
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Comment: C: Perform correlation analysis between miRNA and mRNA gene expression data on the
... Thank you one more time Levi for the feedback and information-i fully understand that the nature and type of normalization is upon me and how i should proceed-the workshop link looks great, so i think that based on your functions and tutorials, subsetting and moving for downstream analysis will not ...
written 3 months ago by svlachavas660
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Comment: C: Perform correlation analysis between miRNA and mRNA gene expression data on the
... Dear Levi, thank you very much for your detailed answer, suggestions and putative steps-some crusial comments: 1) The link above that you have included does not work- so it is possible to search or check which processing steps with which algorithms the assays **"miRNASeqGene"** and **"RNASeq2Gene ...
written 3 months ago by svlachavas660
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Perform correlation analysis between miRNA and mRNA gene expression data on the same TCGA dataset based on the curatedTCGAData
... Dear Community, briefly, based on a previously identified gene signature in a specific type of cancer (through gene expression analysis), in parallel i found also 4 specific microRNAs (mature miRs) that regulate a specific subset of my signature (~18 genes) via experimentally validated databases. ...
tcga multiassayexperiment multiomics curatedtcgadata written 3 months ago by svlachavas660 • updated 3 months ago by Levi Waldron950
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Paired DE analysis in edgeR with trios of samples while blocking for various confounders
... Dear Community, I’m currently analyzing an RNA-Seq gene expression dataset, downloaded from the recount project. It includes trios of paired samples of primary cancers, their liver metastases and their normal adjucent tissue samples (18 patients-54 samples). The code chunk used for downstream anal ...
rnaseq edger design matrix paired analysis written 3 months ago by svlachavas660
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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 4 months ago by svlachavas660
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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 4 months ago by svlachavas660
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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 4 months ago by svlachavas660 • updated 4 months ago by James W. MacDonald50k
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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 5 months ago by svlachavas660
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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 5 months ago by svlachavas660
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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 5 months ago by svlachavas660

Latest awards to svlachavas

Great Question 6 months ago, created a question with more than 5,000 views. For Use of various distance measures and clustering methods in heatmap creation
Popular Question 6 months ago, created a question with more than 1,000 views. For Merge different datasets regarding a common number of DE genes in R
Student 7 months ago, asked a question with at least 3 up-votes. For Appropriate use of the function treat of the limma package
Popular Question 8 months ago, created a question with more than 1,000 views. For Background correction in Illumina beadchip microarrays with limma neqc function
Popular Question 9 months ago, created a question with more than 1,000 views. For Correct assumptions of using limma moderated t-test
Popular Question 9 months ago, created a question with more than 1,000 views. For Error in PCA analysis and with ggbiplot function
Popular Question 11 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 14 months ago, created a question with more than 1,000 views. For Questions in limma about multifactorial design and possible batch effect correction
Student 2.1 years ago, asked a question with at least 3 up-votes. For Appropriate use of the function treat of the limma package
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Problems importing Illumina raw data with lumi R package
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Important r packages not available for R version 3.1.1
Popular Question 2.1 years ago, created a question with more than 1,000 views. For (Gene-set)Pathway analysis based on network/pathway topology in R
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Update R in Rstudio to specific version 3.2.1 in windows

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