User: svlachavas

gravatar for svlachavas
svlachavas570
Reputation:
570
Status:
Trusted
Location:
Greece/Athens/National Hellenic Research Foundation
Last seen:
1 day, 17 hours ago
Joined:
3 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 • 445 results • page 1 of 45 • next >
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Comment: C: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
... Now got the complete point-thank you for your extra comment. ...
written 13 days ago by svlachavas570
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Comment: C: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
... Dear Gordon, thank you for your comment-actually i was confused in the beginning regarding the appropriate interpetation of what logCPM values actually represent-thus, from my understanding-they measure the "overall expression level" of the each transcript-so any log2 cpm value below < 1 would be ...
written 13 days ago by svlachavas570
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Comment: C: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
... Hello Ryan, i had an initial "naive" thought if with increasing the prior.count argument, could reduce the variability of the logCPM values for genes with low counts, but perhaps this could shrunk the values close to zero ? My concern, was for clustering and heatmap creation, if the negative values ...
written 13 days ago by svlachavas570
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Comment: C: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
... Aaron, sorry to return again for this matter, but unfortunately i noticed various negative values in genes, not in all samples but with various frequencies: lihc_filt <- TCGAanalyze_Filtering(tabDF = assay(lihc.exp), method = "quantile",qnt.cut = 0.25) # a small initial filtering from the R pa ...
written 13 days ago by svlachavas570
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Comment: C: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
... Dear Aaron, thank you for your valuable comment about the extra benefit of implementing also the TMM normalization for the downstream EDA analyses. I will also read in detail the relative paper. One small comment i would like to add: for the relative construction of the DGElist object, i could jus ...
written 13 days ago by svlachavas570
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Robust transformation of raw RNA-seq counts for exploratory data analysis and hierarchical clustering
... Dear Community, i would like to ask a more general question about data transformation methodologies, regarding raw RNA-Seq data for exploratory data analysis, and not for DE expression. In detail, i have identified a small 38 gene signature in a specific type of cancer/TCGA dataset, which shows som ...
normalization edger variancestabilizingtransformation cpm rnaseq analysis written 13 days ago by svlachavas570 • updated 10 days ago by Wolfgang Huber13k
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Comment: C: Difficulty in finding DEG using TCGA data from FireBrowse
... Dear Ankita, again with all respect, prior posting any further questions or suggestions, you should firstly make an effort and read or search any tutorials or relative papers related !! thus, you don't trust the answers already above ? if not, why you mention this time the EBSeq R package ? there i ...
written 6 weeks ago by svlachavas570
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Comment: C: Difficulty in finding DEG using TCGA data from FireBrowse
... Dear Akita, with all respect your answer is a bit confusing- why do you mention days to death with Tumor Stage ? these are totally irrelevant fields-it is very important to first define your biological question of interest- moreover, did you find a specific problem with TCGAbiolinks-keep in mind t ...
written 6 weeks ago by svlachavas570
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Answer: A: Difficulty in finding DEG using TCGA data from FireBrowse
... Hello, just to add a small idea in conjuction to Aaron's already complete and detailed answer. If you really want raw counts/data for a specific TCGA project, have you tried the TCGAbiolinks R package ? For example: library(TCGAbiolinks) query.exp.hg38 <- GDCquery(project = "TCGA-STAD", ...
written 6 weeks ago by svlachavas570
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Comment: C: edgeR multifactorial analysis implementation with RNA-Seq data
...  Dear Aaron, nice to hear from you again and thank you for your detailed considerations on this matter !! Actually, i could not agree more, especially for the option 3 of your suggestions, concerning especially the cancer samples. I understand that any NA values in any levels in the design matrix w ...
written 10 weeks ago by svlachavas570

Latest awards to svlachavas

Popular Question 11 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 11 months ago, created a question with more than 1,000 views. For Problems importing Illumina raw data with lumi R package
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 11 months ago, created a question with more than 1,000 views. For Questions in limma about multifactorial design and possible batch effect correction
Popular Question 11 months ago, created a question with more than 1,000 views. For Correct assumptions of using limma moderated t-test
Student 11 months ago, asked a question with at least 3 up-votes. For Appropriate use of the function treat of the limma package
Popular Question 11 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 Important r packages not available for R version 3.1.1
Scholar 12 months ago, created an answer that has been accepted. For A: illuminaHumanv4.db : annotation source, and mapping to transcript names
Popular Question 14 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 14 months ago, created a question with more than 1,000 views. For Merge different datasets and perform differential expression analysis in limma
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Filtering on present/absent calls methodology and perfect match only arrays
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Use of various distance measures and clustering methods in heatmap creation

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