User: thyleal
thyleal • 150
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Posts by thyleal
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... 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
thyleal • 150
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... 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 ...
written 3 days ago by
thyleal • 150
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... 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
thyleal • 150
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... 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
thyleal • 150
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... 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
thyleal • 150
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... Yes, I thought you were only interested in expression biomarkers (mRNA, lncRNA, miRNA etc.). ...
written 10 weeks ago by
thyleal • 150
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... 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
thyleal • 150
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... I agree with @Kelen on trying ORA with the intersection list. ...
written 10 weeks ago by
thyleal • 150
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... 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
thyleal • 150
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... 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
thyleal • 150
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For invalid class NChannelSet object: featureNames differ between assayData and featureData
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