User: svlachavas

gravatar for svlachavas
svlachavas740
Reputation:
740
Status:
Trusted
Location:
Greece/Athens/National Hellenic Research Foundation
Last seen:
3 weeks, 1 day ago
Joined:
4 years, 11 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 • 487 results • page 1 of 49 • next >
1
vote
1
answer
116
views
1
answers
Answer: A: How to perform a differential expression analysis from TCGA file EBPlusPlusAdjus
... Dear KCLiv, if i have understood correctly you have "normalized estimated counts from RSEM" - i have faced previously a similar situation and you can check one of my previous posts with suggested solutions-briefly: https://support.bioconductor.org/p/91054/#95981 1) Continue with the limma-trend p ...
written 9 weeks ago by svlachavas740
1
vote
2
answers
200
views
2
answers
Answer: A: RNASeq DE analysis starts from different DESeq2 normalized data, TMM normalized
... Dear li.zhaoz, it is important before to proceed to read the following posts/articles about rna-seq analysis, normalization and transformation methodologies: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/ https://academic.oup.com/bib/article/14/6/6 ...
written 10 weeks ago by svlachavas740
1
vote
1
answer
123
views
1
answers
Answer: A: Finding gene targets for a list of transcription factors
... Dear Anita, even your question is not directly related to the purpose of this group, i would quickly suggest for a solution through R/Bioconductor the R package CoRegNet [http://bioconductor.org/packages/release/bioc/html/CoRegNet.html]-but the relative gene expression data are necessary for the c ...
written 11 weeks ago by svlachavas740
0
votes
1
answer
187
views
1
answers
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 8 months ago by svlachavas740
0
votes
1
answer
187
views
1
answers
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 8 months ago by svlachavas740
4
votes
1
answer
187
views
1
answer
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 8 months ago by svlachavas740 • updated 8 months ago by Levi Waldron980
0
votes
0
answers
135
views
0
answers
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 8 months ago by svlachavas740
0
votes
1
answer
182
views
1
answers
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 9 months ago by svlachavas740
0
votes
1
answer
182
views
1
answers
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 9 months ago by svlachavas740
1
vote
1
answer
182
views
1
answer
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 9 months ago by svlachavas740 • updated 9 months ago by James W. MacDonald52k

Latest awards to svlachavas

Great Question 11 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 11 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 12 months ago, asked a question with at least 3 up-votes. 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 Background correction in Illumina beadchip microarrays with limma neqc function
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 Error in PCA analysis and with ggbiplot function
Popular Question 16 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 19 months ago, created a question with more than 1,000 views. For Questions in limma about multifactorial design and possible batch effect correction
Student 2.5 years ago, asked a question with at least 3 up-votes. For Appropriate use of the function treat of the limma package
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Problems importing Illumina raw data with lumi R package
Popular Question 2.5 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 2.5 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 2.5 years ago, created a question with more than 1,000 views. For Update R in Rstudio to specific version 3.2.1 in windows

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 220 users visited in the last hour