User: thyleal

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thyleal150
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Posts by thyleal

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Comment: C: Compare pathway activation across microarray datasets?
... Thanks for the suggestion. The score you refer as output of the `geneSetTest` function in limma is a P-value, right? ...
written 3 days ago by thyleal150
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Compare pathway activation across microarray datasets?
... Dear colleagues, I have some microarray datasets with distinct diseases in each of them and I'd like to generate a score to indicate activity of a given pathway in a way comparable across datasets. Most of them are the same Affymetrix platform, but not all. I started by reanalyzing each from scra ...
normalization microarray scores written 3 days ago by thyleal150
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Answer: A: Linear regression of the RNAseq results to get the genes whose expression change
... Hi, About your error: you probably mistyped the name argument in your second line of code here. Use resultsNames(ddsTC) to see available names. About the analysis, you seem to want to test this in two distinc ways. One testing for any differences over multiple stages, exactly what you did with the ...
written 8 weeks ago by thyleal150
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Answer: A: how to compare two gene lfc rank is similar or opposite ?
... You want to compare gene's modulation between two comparisons, right? Your lists look ordered, but they do not look like ranks (expecting integers). If you want work with ranks, see RankProd or RankSum approaches. Also, check these: https://www.bioconductor.org/packages/release/bioc/vignettes/Order ...
written 8 weeks ago by thyleal150
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Comment: C: Specify coefficient results group on dds in DESEq2
... Yes, exactly what @Carlo said. If you need to control all levels, just use `x <- factor(y, levels = c(level1, level2, level3, leveln))` ...
written 10 weeks ago by thyleal150
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Comment: C: Current best practice for biomarker discovery using transcriptomics data
... Yes, I thought you were only interested in expression biomarkers (mRNA, lncRNA, miRNA etc.). ...
written 10 weeks ago by thyleal150
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Comment: C: Current best practice for biomarker discovery using transcriptomics data
... Sure, take a look: - http://dx.doi.org/10.1016/j.ymeth.2012.08.012 - 10.3389/fgene.2020.00019 - 10.1186/s13045-020-01005-x - 10.2217/bmm.15.16 - https://rna-seqblog.com/tag/biomarker-discovery/ (good collection of posts) - 10.3389/fimmu.2019.00221 - 10.6026/97320630014153 If I remember mor ...
written 10 weeks ago by thyleal150
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Comment: C: GSEA Pre-ranked for an Overlapped Gene Set
... I agree with @Kelen on trying ORA with the intersection list. ...
written 10 weeks ago by thyleal150
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Answer: A: Current best practice for biomarker discovery using transcriptomics data
... I never came across such tutorial... If you are familiar with RNAseq data analysis for differential expression, you can follow from there. What I often see is: - Exploratory data analysis and quality control (PCA, MDS, sanity checks etc); - Differential gene/transcript analysis (interesting to se ...
written 10 weeks ago by thyleal150
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Answer: A: Specify coefficient results group on dds in DESEq2
... You can relevel your factor variable and specify your group 1 in the first position instead of group 5. For example, group1, group2, group3, group4, group5, group6, group7. This would natively include a coefficient comparing group7_vs_group1. ...
written 10 weeks ago by thyleal150

Latest awards to thyleal

Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Current best practice for biomarker discovery using transcriptomics data
Scholar 7 weeks ago, created an answer that has been accepted. For A: Current best practice for biomarker discovery using transcriptomics data
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Problem Annotation Construction with pdInfoBuilder - Microarray Bioconductor
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Current best practice for biomarker discovery using transcriptomics data
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