User: glocke01

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glocke01160
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Posts by glocke01

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Download all DNA mutations from TCGA
... try https://portal.gdc.cancer.gov/repository ...
written 6 weeks ago by glocke01160
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Comment: C: how do I properly use edgeR::scaleOffset to combine two targeted RNA-seq panels?
... thanks once again, Prof. Smyth!! ...
written 9 weeks ago by glocke01160
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Comment: C: differential gene set testing combining genes from multiple panels
... Thanks again, Gordon. I'm not sure that I'm using `scaleOffset` correctly, and I've asked another question requesting further assistance. https://www.biostars.org/p/370793/ Any help from you or Aaron or anyone would be great. ...
written 9 weeks ago by glocke01160
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how do I properly use edgeR::scaleOffset to combine two targeted RNA-seq panels?
... I am trying to analyze some targeted RNA-seq data, where for each sample/mouse I have data from two panels. Because there are two panels, the data for each sample effectively have two library sizes. This means I can't just rbind the two panels together and use a normal RNA seq workflow. In principle ...
panel rna-seq edger written 9 weeks ago by glocke01160
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Comment: C: differential gene set testing combining genes from multiple panels
... awesome, thanks!! ...
written 9 weeks ago by glocke01160
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differential gene set testing combining genes from multiple panels
... I have RNA-seq data from two targeted panels. So, for each sample/mouse, I have one counts matrix for one set of genes, and another matrix for another set of genes. The major problem here is that the library size for a given sample is different across the two panels, so just slapping the two matrice ...
pathway limma rna-seq voom written 9 weeks ago by glocke01160 • updated 9 weeks ago by Gordon Smyth780
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Comment: C: GSEA top genes vs all platform
... You can also use gene set tests included in the limma package, i.e. CAMERA and ROAST. CAMERA, in particular, is way, way faster than GSEA. Prof. Smyth has made the MSigDB gene sets available in easy to ingest .rda files at his website: http://bioinf.wehi.edu.au/software/MSigDB/index.html ...
written 9 months ago by glocke01160
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Comment: C: Pathway test for reversal of effect (three-condition comparison)
... I think a geometric/harmonic average might be appropriate (as opposed to the arithmetic mean implicit in my SNR statistic) so that small values in either comparison would strongly penalize the final statistic... ...
written 9 months ago by glocke01160
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Comment: C: Pathway test for reversal of effect (three-condition comparison)
... Nice. Good thinking: rank based on some relevant comparison, send ranks to GSEA or suchlike. I guess the trouble is defining a single number for ranking purposes - by signal to noise, I take it you're thinking something like `(mean in A minus mean in AB and ∅)/stdev(all samples)`. Something like av ...
written 9 months ago by glocke01160
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Comment: C: Pathway test for reversal of effect (three-condition comparison)
... It's relatively simple to describe what I'm looking for as "effects of `A` reversed by `B`", but I am aware that that language is substantively imprecise - literal reversal would be treating with `A` then `B`. The biological question of interest would be more accurately described as "effects of `A - ...
written 10 months ago by glocke01160

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Great Question 3 months ago, created a question with more than 5,000 views. For How can I shuffle a set of sequences while preserving the dinucleotide distribution?
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