User: svlachavas

gravatar for svlachavas
svlachavas390
Reputation:
390
Status:
Trusted
Location:
Greece/Athens/National Hellenic Research Foundation
Last seen:
8 hours ago
Joined:
2 years 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 • 390 results • page 1 of 39 • next >
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Oh my mistake for forgetting the initial transformation regarding the filtering. Also please excuse me for the possible misunderstanding-not intented to ask for other kind of help or irrelevant suggestions of this topic-just asked it for a quick confirmation about any similar example ( i just menti ...
written 4 days ago by svlachavas390
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Thank you one more time for your updated example !! two quick comments to add: 1) you mentioned in the filtering part  keep <- rowSums(y > log2(11)) >= 14 but you used log2(11) instead of y>11 ? or it is just a typo ? 2) a more statistical question but vital: [due to one very intere ...
written 5 days ago by svlachavas390
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Dear Gordon, thank you again for your updated recommendations !! so the above are two available methodologies to use/test--just a small comment regarding the direct approach with the log2 transformed counts : xx <- TCGA.RNASeqV2_eset set <- exprs(xx) set.norm <- normalizeQuantiles(set) ...
written 6 days ago by svlachavas390
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Dear Levi, thank you one more time for your updated answers. From the following link (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/) perhaps the reference genome is the one mentioned GRCh38-Nevertheless, it probably best checking an individual sample, but again ...
written 7 days ago by svlachavas390
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Dear Gordon, thank you for your consideration and suggestions on this matter !! Regarding the second part of your answer, you mean to feed directly the above transformed log2(counts+1) in limma -like the microarrays pipeline (limFit, eBayes) without any other transformations/normalization from the R ...
written 7 days ago by svlachavas390
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Dear Levi, thank you again for your valuable comments and confirmation of Steves suggestion. 3 final comments to summarize in order to be certain and close this topic: 1) i checked the description file above, as also the original paper publication. Thus, by the above tranformation, i get the "raw e ...
written 8 days ago by svlachavas390
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Dear Steve, thank you for your comment and idea--yes the min is zerro: range(exprs(TCGA.RNASeqV2_eset)) [1]  0.00000 20.34961 However, i don't know if the below log2 transformation [if the maximum value is greater than 50] could be reversed with your suggestion-perhaps it is different from the g ...
written 8 days ago by svlachavas390
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Dear Michael, thank you for your useful answer and recommendations !! Indeed the numbers in the matrix have confused me a lot, but from the initial contact with the maintainers of the package, they mentioned that these are level 3 TCGA RNA-Seq data from RSEM. I have also checked the following links ...
written 8 days ago by svlachavas390
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Chris thank you for your answer !! i have seen also the EBSEQ !! unfortunately, there is not a clear answer to this specific problem, so i hope with this post i get any suggestions to take all the possible options into account !!   ...
written 8 days ago by svlachavas390
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Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
... Dear BiocCommunity, i have imported from the R package curatedCRCdata, an RNA-Seq dataset regarding a specific type of cancer. In detail, after contacting the maintainers of the package, they kindely provided the information, that the data are IlluminaHiSeq_RNASeqV2 Level 3 data, which were quantif ...
edger tcga normalization rsem rnaseq written 8 days ago by svlachavas390 • updated 7 days ago by Gordon Smyth29k

Latest awards to svlachavas

Popular Question 10 months ago, created a question with more than 1,000 views. For Error in PCA analysis and with ggbiplot function
Scholar 15 months ago, created an answer that has been accepted. For A: illuminaHumanv4.db : annotation source, and mapping to transcript names
Voter 15 months ago, voted more than 100 times.
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: MAS 5 package
Scholar 18 months ago, created an answer that has been accepted. For A: MAS 5 package
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: MAS 5 package
Scholar 19 months ago, created an answer that has been accepted. For A: MAS 5 package
Autobiographer 19 months ago, has more than 80 characters in the information field of the user's profile.
Centurion 21 months ago, created 100 posts.
Supporter 22 months ago, voted at least 25 times.
Rising Star 22 months ago, created 50 posts within first three months of joining.

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