Moderator: Kevin Blighe

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Kevin Blighe66k
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3 years, 1 month ago
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k****@clinicalbioinformatics.co.uk

Posts by Kevin Blighe

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Comment: C: How to plot figure?
... The bottom part is just a heatmap - check the methods to see what it says. Then, the entire figure panels are likely pieced together manually ...
written 10 days ago by Kevin Blighe66k
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Comment: C: volcano plot not showing genera name clearly
... Use the FDR column instead of the nominal p-value column. ...
written 12 days ago by Kevin Blighe66k
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Comment: C: getBM error while using bioMart
... I see. What is the output of: str(TPM_countdata$ensembl) ? Also, from where are you running this command (on a cluster)? ...
written 16 days ago by Kevin Blighe66k
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Comment: C: getBM error while using bioMart
... Hi, can you please try just: ensembl = useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl") Also, which version of R and *biomaRt* are you using? ...
written 16 days ago by Kevin Blighe66k
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Comment: C: PCA plots and biological information taken from other principal components
... Yes, *PCAtools* can do this: Determine the variables that drive variation among each PC But, let me know how you have currently done your PCA? ...
written 16 days ago by Kevin Blighe66k
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Answer: A: Reorganize the clusters
... Boa tarde, Tem que definir os agrupamentos fora do função `Heatmap()`, como faço aqui: / You have to define the clusters outside of the `Heatmap()` function, as I do here: - https://github.com/kevinblighe/E-MTAB-6141 Depois/ Then (after), follow the advice here: https://www.biostars.org/p/306473 ...
written 18 days ago by Kevin Blighe66k
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Comment: C: heatmap for coding and noncoding genes
... Thank you Sir. You got it working? ...
written 19 days ago by Kevin Blighe66k
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Comment: C: heatmap for coding and noncoding genes
... Please see the vignette, which I personally wrote: https://bioconductor.org/packages/devel/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html#over-ride-colour-andor-shape-scheme-with-custom-key-value-pairs ...
written 20 days ago by Kevin Blighe66k
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Comment: C: Resources for gene signature creation
... I am sorry - this is difficult for me to debug while remote. You will have to go back through your code. Keep in mind that this type of work is quite advanced. ...
written 20 days ago by Kevin Blighe66k
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Comment: C: Resources for gene signature creation
... That is for the cross-validated R2? What was the output of `DAAG::cv.lm`? You could avoid `crossval()` for now. How does the plot for Predicted versus Real values appear? ...
written 20 days ago by Kevin Blighe66k

Latest awards to Kevin Blighe

Appreciated 5 days ago, created a post with more than 5 votes. For A simple tutorial for a complex ComplexHeatmap
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: problem in generating correlation heatmap with significance level
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: problem in generating correlation heatmap with significance level
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: problem in generating correlation heatmap with significance level
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: problem in generating correlation heatmap with significance level
Scholar 21 days ago, created an answer that has been accepted. For A: How do I subset VCF based on genotype?
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: problem in generating correlation heatmap with significance level
Scholar 21 days ago, created an answer that has been accepted. For A: How do I subset VCF based on genotype?
Scholar 22 days ago, created an answer that has been accepted. For A: How do I subset VCF based on genotype?
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: What is the best way to combine machine learning algorithms for feature selectio
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: problem in generating correlation heatmap with significance level
Scholar 22 days ago, created an answer that has been accepted. For A: How to convert gallus gallus entrezID into human entrezID
Scholar 22 days ago, created an answer that has been accepted. For A: How do I subset VCF based on genotype?
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: problem in generating correlation heatmap with significance level
Scholar 23 days ago, created an answer that has been accepted. For A: How do I subset VCF based on genotype?
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: problem in generating correlation heatmap with significance level
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: What is the best way to combine machine learning algorithms for feature selectio
Scholar 27 days ago, created an answer that has been accepted. For A: How do I subset VCF based on genotype?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: What is the best way to combine machine learning algorithms for feature selectio
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: What is the best way to combine machine learning algorithms for feature selectio
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to convert gallus gallus entrezID into human entrezID
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: What is the best way to combine machine learning algorithms for feature selectio
Scholar 5 weeks ago, created an answer that has been accepted. For A: Converting HGNC to ensembl and entrez id's using biomart
Gold Standard 5 weeks ago, created a post with more than 25 bookmarks. For Survival analysis with gene expression

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