User: svlachavas

gravatar for svlachavas
svlachavas570
Reputation:
570
Status:
Trusted
Location:
Greece/Athens/National Hellenic Research Foundation
Last seen:
1 month, 1 week ago
Joined:
3 years, 1 month 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 • 434 results • page 1 of 44 • next >
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Comment: C: Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dat
... Thanks Aaron for the update. The simpler the better. ...
written 11 weeks ago by svlachavas570
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Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
... Dear Community, i would like to annotate a created DGEList object using the DGEList function from the edgeR function,with unique gene symbols for ensemble identifiers. My approach is the following : y <- DGEList(counts=assay(coad_clear), group=colData(coad_clear)$definition) head(y$counts[1: ...
edger org.hs.eg.db dgelist gene annotation written 11 weeks ago by svlachavas570 • updated 11 weeks ago by Aaron Lun18k
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Comment: C: Error and weird result of TCGAanalyze_Normalization function using the R package
... Dear Antonio, thank you for your consideration on this matter and also your anwer in the github group and relative discussion !! please excuse me for also adressing a similar issue here, and not for the reason that your answer did not help me for the first part-but mainly for adressing more a secon ...
written 12 weeks ago by svlachavas570
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Comment: C: Error and weird result of TCGAanalyze_Normalization function using the R package
... Thank you for your answer Davide and please excuse me for the misinprentation of the above function. I saw also in section 8 of the vignette the function getGeneLengthAndGCContent , from which i probably will retreive the gc content for my ensembl identifiers of the datasets. ...
written 12 weeks ago by svlachavas570
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Specific considerations in RNA-Seq DE analysis with edgeR pipeline for a TCGA dataset starting with HTSeq counts
... Dear BioCommunity, i have downloaded raw HTSeq counts for a provisional cancer TCGA dataset, with the R package TCGAbiolinks. My main goal is to implement DE expression analysis for a two-group comparison with edgeR pipeline, especially with the TREAT approach implementation, to inspect the overlap ...
rnaseq edger independent filtering tcga deanalysis written 12 weeks ago by svlachavas570
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Comment: C: Error and weird result of TCGAanalyze_Normalization function using the R package
... Dear Davide, please excuse me to return on this post, but unfortunately, a weird error appeared when i tried to use the above function: gcounts <- assay(exp.hg38) class(gcounts) [1] "matrix" dnorm <- withinLaneNormalization(x=gcounts, which="full") Error in (function (classes, fdef, mtable ...
written 12 weeks ago by svlachavas570
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Comment: C: Error and weird result of TCGAanalyze_Normalization function using the R package
... Thanks Davide. I will take a detailed look and perhaps write back or on a different thread for possible related questions. ...
written 3 months ago by svlachavas570
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Comment: C: Error and weird result of TCGAanalyze_Normalization function using the R package
... Dear davide, thank you for your updated answer. Firstly, concerning the geneInfo object head(geneInfo)           geneLength gcContent           chr     100130426 NA         NA                  ""      100133144 "2420"     "0.490495867768595" "chr15" 100134869 "3190"     "0.428526645768025" "chr15 ...
written 3 months ago by svlachavas570
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Comment: C: Error and weird result of TCGAanalyze_Normalization function using the R package
... Dear Davide, thank you for your responce and consideration on this matter !! Firstly, based on your question, the geneInfo argument above, has 2 options to consider: xx <- TCGAbiolinks::geneInfo > head(xx)           geneLength gcContent           chr     100130426 NA         NA              ...
written 3 months ago by svlachavas570
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Error and weird result of TCGAanalyze_Normalization function using the R package TCGAbiolinks for normalization of raw HTSeq counts
... Dear BioCommunity, i recently implemented the R package TCGAbiolinks, to download raw HTSEQ counts for a provinsional cancer TCGA dataset (COAD). My code used was the following: query.exp.hg38 <- GDCquery(project = "TCGA-COAD",  data.category = "Transcriptome Profiling",  data.type = "Gene Expr ...
rnaseq normalization edaseq tcgabiolinks written 3 months ago by svlachavas570 • updated 12 weeks ago by antonio.colaprico40

Latest awards to svlachavas

Scholar 9 months ago, created an answer that has been accepted. For A: illuminaHumanv4.db : annotation source, and mapping to transcript names
Popular Question 11 months ago, created a question with more than 1,000 views. For Merge different datasets and perform differential expression analysis in limma
Popular Question 11 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 22 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 22 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 22 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 22 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 22 months ago, created a question with more than 1,000 views. For Appropriate use of the function treat of the limma package
Popular Question 22 months ago, created a question with more than 1,000 views. For Correct assumptions of using limma moderated t-test
Popular Question 22 months ago, created a question with more than 1,000 views. For Error in PCA analysis and with ggbiplot function
Popular Question 23 months ago, created a question with more than 1,000 views. For Error in PCA analysis and with ggbiplot function
Scholar 2.3 years ago, created an answer that has been accepted. For A: illuminaHumanv4.db : annotation source, and mapping to transcript names
Voter 2.4 years ago, voted more than 100 times.
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: MAS 5 package
Scholar 2.6 years ago, created an answer that has been accepted. For A: MAS 5 package
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: MAS 5 package
Scholar 2.7 years ago, created an answer that has been accepted. For A: MAS 5 package

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