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Moderator: Kevin Blighe

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Kevin Blighe ♦ 69k
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Republic of Ireland
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https://kevinblighe.co...
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3 months ago
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Posts by Kevin Blighe

<prev • 9,137 results • page 1 of 914 • next >
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Comment: C: GO analysis using topGO
... Thank you - I have made the change ...
written 14 hours ago by Kevin Blighe ♦ 69k
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Comment: C: build the expression matrix step by step from GEO raw data
... You can filter probes prior to or after normalisation in any microarray analysis pipeline. The above code is generic and it's expected that one adapts this to their own data. The limma user guide has much more information: https://bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/ ...
written 3 days ago by Kevin Blighe ♦ 69k
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Comment: C: Module trait association in wgcna
... In my code, `pink_module` would contain the module values returned by WGCNA, with there being 1 value per sample. Yes, `mydata` would be of the form that you have shown, but also including extra columns for the modules (pink, blue, green, etc) ...
written 3 days ago by Kevin Blighe ♦ 69k
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Answer: A: Module trait association in wgcna
... I think that you are doing it correctly. I would use a binary logistic regression model here, something like: summary(glm(timezone1 ~ pink_module, data = mydata, family = binomial(link = 'logit'))) You can also just perform a numerical correlation: cor(as.numeric(mydata$pink_module), myda ...
written 3 days ago by Kevin Blighe ♦ 69k
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Comment: C: Cannot convert gene ID to gene symbol
... They will usually be left in the dataset, even after normalisation. However, these probes should begin with AFFX or BGP - see here: https://www.biostars.org/p/167209/#273842 ...and you should indeed remove these after normalisation. ...
written 3 days ago by Kevin Blighe ♦ 69k
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Answer: A: Cannot convert gene ID to gene symbol
... Yes, predicted genes may not necessarily have yet been assigned an ID by Ensembl, Entrez, HGNC, et cetera. This probe genuinely has no matches: require('hgu133plus2.db') annotLookup <- select(hgu133plus2.db, keys = c('1563061_at'), columns = c('PROBEID', 'ENSEMBL', 'SYMBOL', 'ENT ...
written 3 days ago by Kevin Blighe ♦ 69k
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Comment: C: WGCNA negative values
... Well, there may be the problem. Your data frame is encoded categorically, i.e., as factors. You need to convert it to a data matrix or to keep it as a data frame but with everything encoded numerically. ...
written 4 days ago by Kevin Blighe ♦ 69k
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Comment: C: Does GSVA normalize sampleset?
... Yes, I believe some methods result in further normalisation / transformation. This information can [I believe] be read in the manual pages. Thank you for posting an answer. ...
written 4 days ago by Kevin Blighe ♦ 69k
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Answer: A: How can I visualize the Pileup to determine if there is a 5 BP deletion?
... Just adding an alternative answer for others: samtools tview Kevin ...
written 4 days ago by Kevin Blighe ♦ 69k
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Comment: C: Creating a cls file from two groups of TCGA RNA-seq samples
... Oh, I see what you mean. Do you have a sample of the input data that you've got? ...
written 4 days ago by Kevin Blighe ♦ 69k

Latest awards to Kevin Blighe

Teacher 17 hours ago, created an answer with at least 3 up-votes. For A: problem in generating correlation heatmap with significance level
Appreciated 3 days ago, created a post with more than 5 votes. For EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
Appreciated 4 days ago, created a post with more than 5 votes. For A simple tutorial for a complex ComplexHeatmap
Appreciated 6 days ago, created a post with more than 5 votes. For A simple tutorial for a complex ComplexHeatmap
Scholar 6 days ago, created an answer that has been accepted. For A: How do I subset VCF based on genotype?
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: problem in generating correlation heatmap with significance level
Scholar 8 days ago, created an answer that has been accepted. For A: How do I subset VCF based on genotype?
Good Answer 12 days ago, created an answer that was upvoted at least 5 times. For A: What is the best way to combine machine learning algorithms for feature selectio
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: problem in generating correlation heatmap with significance level
Good Answer 20 days ago, created an answer that was upvoted at least 5 times. For A: What is the best way to combine machine learning algorithms for feature selectio
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: problem in generating correlation heatmap with significance level
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: problem in generating correlation heatmap with significance level
Good Answer 23 days ago, created an answer that was upvoted at least 5 times. For A: What is the best way to combine machine learning algorithms for feature selectio
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: problem in generating correlation heatmap with significance level
Scholar 24 days ago, created an answer that has been accepted. For A: How to Interpret p-value from multi-curve Kaplan-Meier Graph
Scholar 24 days ago, created an answer that has been accepted. For A: How do I subset VCF based on genotype?
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: problem in generating correlation heatmap with significance level
Scholar 25 days ago, created an answer that has been accepted. For A: How do I subset VCF based on genotype?
Appreciated 25 days ago, created a post with more than 5 votes. For Why do PCA+tSNE/viSNE or PCA+UMAP, and not just tSNE/viSNE or UMAP on their own?
Scholar 28 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: problem in generating correlation heatmap with significance level
Scholar 4 weeks ago, created an answer that has been accepted. For A: How do I subset VCF based on genotype?
Appreciated 5 weeks ago, created a post with more than 5 votes. For Why do PCA+tSNE/viSNE or PCA+UMAP, and not just tSNE/viSNE or UMAP on their own?
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: What is the best way to combine machine learning algorithms for feature selectio
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: problem in generating correlation heatmap with significance level
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