Moderator: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe61k
Reputation:
60,960
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Location:
University College London
Website:
https://github.com/kev...
Twitter:
KevinBlighe
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Google Scholar Page
Last seen:
4 hours ago
Joined:
2 years, 10 months ago
Email:
k****@clinicalbioinformatics.co.uk

I am from the Republic of Ireland and have worked with dozens of universities, private companies, healthcare providers, and research institutes across the World, effectively functioning as a self-funded, independent research lab.

I contribute to the European Commission as an Expert Monitor, and also Moderate on the Biostars and Bioconductor support communities.
 

Developer / Maintainer of Bioconductor packages:

Other packages:

LinkedIn: https://www.linkedin.com/in/clinicalbioinformatics/

 

Posts by Kevin Blighe

<prev • 8,375 results • page 2 of 838 • next >
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Comment: C: Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) : HDF5. File access
... > Based on what I read re: this exact error, it was not the code I was > running but the system I was running kalliso on when the h5 files were > created Yep, that's the conclusion that I got, too. The error has been reported a few times, as you mention, but no definitive solution or exact ...
written 2 days ago by Kevin Blighe61k
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Comment: C: If I have a ran-seq data of disease A and also rna-seq for disease B on the same
... Cool. You should be doing pathway analysis on these diseases too, in that case, and checking for overlapping pathways (and noting the pathways that differ). ...
written 2 days ago by Kevin Blighe61k
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Comment: C: If I have a ran-seq data of disease A and also rna-seq for disease B on the same
... Sure, but, are these diseases completely different or are they sub-types of the same disease? It is not a problem to simply compare the 2 lists of the genes that are statistically significant. What do you ultimately hope to infer from this particular part of the analysis? For a simple meta-analysis ...
written 2 days ago by Kevin Blighe61k
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Answer: A: GSVA kernels: Gaussian or Poisson?
... It really does just depend on the distribution of the input data, which you already appear to understand. The default of Gaussian is set thus due to the fact that most downstream datasets that are using GSVA will have already been normalised and transformed to a Gaussian. If I were using FPKM, RPKM, ...
written 3 days ago by Kevin Blighe61k
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Answer: A: If I have a ran-seq data of disease A and also rna-seq for disease B on the same
... Yes; however, the way that you report on the results (the overlapping / common genes) is important. You could 'formalise' the overlap by doing a meta analysis. Also, if all samples were profiled together in the same experiment, it would be better to process and normalise these together, and also pe ...
written 3 days ago by Kevin Blighe61k
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... Hey, > Q1:In "step7, Prune variants from each chromosome", why don't you > exclude long high-LD regions? Isn't that necessary? You can do that. Actually, pruning for LD is performed via the `--indep` flag (see your question 4) > Q2: 1)a. Prune 1kg and my own dataset respectively ; b. Mer ...
written 3 days ago by Kevin Blighe61k
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Comment: C: Clustering of DAVID gene enrichment results from gene expression studies
... Hello Suren, the gene score is the negative log10 of the adjusted p-value for each gene, calculated in this line: dfMinusLog10FDRGenes <- data.frame(-log10( topTableAligned[which(rownames(topTableAligned) %in% rownames(annGSEA)), 'padj'])) ...
written 4 days ago by Kevin Blighe61k
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Comment: C: Survival analysis with gene expression
... For that part, which is somewhat outside of my knowledge area, you may want to ask a question on a stats forum, like CrossValidated. I am actually only relatively recently working in internal and external calibration, so, I do not feel it is my place to provide advice right now. ...
written 4 days ago by Kevin Blighe61k
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Comment: C: What is the story behind chrEBV?
... I don't use PubMed for searching. Any other search engine is better. For searching for papers within PubMed, just use the `ncbi` keyword first in your search string. ...
written 4 days ago by Kevin Blighe61k
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Answer: A: BATCH EFFECT REMOVAL
... > Q - 1. I had read that the batch effect removal algorithm is required > when your approach is "Data Merging" and not "Meta-analysis". I hadn't > merged my data - Just performed limma analysis and then check for > common genes and finally used the pval combination method. Finally, > ...
written 4 days ago by Kevin Blighe61k

Latest awards to Kevin Blighe

Good Answer 8 hours ago, created an answer that was upvoted at least 5 times. For A: PCA: summarize results from principal components analysis and look for populatio
Appreciated 10 hours ago, created a post with more than 5 votes. For A simple tutorial for a complex ComplexHeatmap
Scholar 2 days ago, created an answer that has been accepted. For A: Correcting for population structure in GWAS?
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Correcting for population structure in GWAS?
Commentator 5 days ago, created a comment with at least 3 up-votes. For C: bash and awk code
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Correcting for population structure in GWAS?
Good Answer 11 days ago, created an answer that was upvoted at least 5 times. For A: How to plot a heatmap with two different distance matrices for X and Y
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Correcting for population structure in GWAS?
Scholar 14 days ago, created an answer that has been accepted. For A: Design in DESeq: Can you combine explicit and implicit batch effect correction i
Popular Question 15 days ago, created a question with more than 1,000 views. For The push toward standardisation
Scholar 16 days ago, created an answer that has been accepted. For A: Design in DESeq: Can you combine explicit and implicit batch effect correction i
Scholar 16 days ago, created an answer that has been accepted. For A: Design in DESeq: Can you combine explicit and implicit batch effect correction i
Good Answer 19 days ago, created an answer that was upvoted at least 5 times. For A: How to plot a heatmap with two different distance matrices for X and Y
Good Answer 20 days ago, created an answer that was upvoted at least 5 times. For A: How to plot a heatmap with two different distance matrices for X and Y
Commentator 21 days ago, created a comment with at least 3 up-votes. For C: bash and awk code
Scholar 22 days ago, created an answer that has been accepted. For A: Design in DESeq: Can you combine explicit and implicit batch effect correction i
Appreciated 26 days ago, created a post with more than 5 votes. For A: Z score in RNAseq
Appreciated 27 days ago, created a post with more than 5 votes. For A: Z score in RNAseq
Scholar 28 days ago, created an answer that has been accepted. For A: DeSeq2 error: Every gene contains at least one zero, cannot compute log geometri
Appreciated 28 days ago, created a post with more than 5 votes. For A: Z score in RNAseq
Appreciated 29 days ago, created a post with more than 5 votes. For A: Z score in RNAseq
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: DeSeq2 error: Every gene contains at least one zero, cannot compute log geometri

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