User: svlachavas

gravatar for svlachavas
svlachavas420
Reputation:
420
Status:
Trusted
Location:
Greece/Athens/National Hellenic Research Foundation
Last seen:
11 hours ago
Joined:
2 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 • 408 results • page 1 of 41 • next >
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Comment: C: Possible approach of compare/interpret RNA-Seq results with microarray gene expr
... Dear Aaron, sorry to return after some days, just a small update and your comment on the final interpretation. Briefly, based on your relative comments: head(vec1) [1] "AARS"   "ABCD3"  "ACADM"  "ACADS"  "ACADVL" "AHCY"  # the vector of common DE gene symbols  head(genes.fc.vec1) [1]  0.7871676 - ...
written 1 day ago by svlachavas420
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Answer: A: illumina ht-12 v4 expression beadchip
... Just to extend Chris answer, the R package BeadArrayUseCases (http://bioconductor.org/packages/release/data/experiment/html/BeadArrayUseCases.html) has a very extensive vignette especially for Illumina platforms. ...
written 1 day ago by svlachavas420
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Comment: C: Appropriate design matrix set up in limma for 2-factor approches with NA values
... Thank you Steve for your answer !! ...
written 5 days ago by svlachavas420
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Comment: C: Appropriate design matrix set up in limma for 2-factor approches with NA values
... Thank you Gordon for the confirmation. I will probably stick and subset the initial dataset, in order to formulate the above mentioned comparison, than perhaps mess up things with adding arbitary values. Finally, do you believe that any non-specific intensity procedure for removing "unexpressed" gen ...
written 6 days ago by svlachavas420
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Dear Gordon, please excuse me to return after a rather long period-however, based on some search to verify the pre-processing details of this dataset, it seems that the estimated counts are probably not log2(raw_estimated_counts +1), but log2(normalized_results +1).  From a small search, these no ...
written 7 days ago by svlachavas420
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Appropriate design matrix set up in limma for 2-factor approches with NA values for specific levels
... Based on an initial analysis of a TCGA RNA-Seq dataset(processed like microarrays), i would like to formulate a specific design matrix with limma, in order to perform a 2-factor type analysis. In detail, a subset of my phenoData object: head(pdat.sel)                 sample_type age_at_initial_path ...
limma design and contrast matrix na values multiple factor design written 7 days ago by svlachavas420 • updated 6 days ago by Gordon Smyth30k
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Comment: C: Weird error with raw data using function boxplot after importing Affymetrix Huma
... Dear James,  thank you again for your answer and comprehensive example !! Although i have read extensively about eSet containers, especially with the Affy package, but it seems that i have encoutered this problem with the oligo R package for the first time-also regarding the possible choises you su ...
written 8 days ago by svlachavas420
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Comment: C: Weird error with raw data using function boxplot after importing Affymetrix Huma
... Dear James,  thank you for your answer and suggestions-regarding your comment about phenoData object, i procedeed as above, because of other errors initially appeared--but i have checked consistently that the rownames of the pdat object are identical and in the same order with the row names of the ...
written 8 days ago by svlachavas420
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Weird error with raw data using function boxplot after importing Affymetrix Human ST 2.0 CEL files with oligo
... Dear Community, based on the code presented on a previous post, regarding the import and analysis of Affymetrix Human ST 2.0 microarrays (https://support.bioconductor.org/p/91931/), i tried to create some exploratory diagnostic plots regarding the success of normalization, for a needed report: lib ...
microarray oligo affymetrix human st arrays hugene20sttranscriptcluster.db written 9 days ago by svlachavas420 • updated 8 days ago by James W. MacDonald42k
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Comment: C: Possible approach of compare/interpret RNA-Seq results with microarray gene expr
... oh i think i got it-so provide a total vector of gene symbols in the index, as also the total relative log2FCs in the gene.weights argument, correct ? and then from the proportion of up and down genes, i should interpret in the same way the consistensy of this signature in the tested dataset, right ...
written 9 days ago by svlachavas420

Latest awards to svlachavas

Popular Question 10 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 10 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 10 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 10 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 10 months ago, created a question with more than 1,000 views. For Appropriate use of the function treat of the limma package
Popular Question 10 months ago, created a question with more than 1,000 views. For Correct assumptions of using limma moderated t-test
Popular Question 10 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 Error in PCA analysis and with ggbiplot function
Scholar 16 months ago, created an answer that has been accepted. For A: illuminaHumanv4.db : annotation source, and mapping to transcript names
Voter 16 months ago, voted more than 100 times.
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
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: MAS 5 package
Scholar 20 months ago, created an answer that has been accepted. For A: MAS 5 package
Autobiographer 20 months ago, has more than 80 characters in the information field of the user's profile.
Centurion 22 months ago, created 100 posts.
Supporter 23 months ago, voted at least 25 times.
Rising Star 24 months ago, created 50 posts within first three months of joining.

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