User: andrew.j.skelton73

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Posts by andrew.j.skelton73

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Comment: C: interactive pathway analysis with fold change data
... The only pathway analysis software I know of that leverages directionality and magnitude is Ingenuity Pathway Analysis. I'd be very happy to know of some alternatives though! ...
written 6 days ago by andrew.j.skelton733.7k
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Comment: C: Perform differential expression for illumina data
... Limma is currently at version 3.32.5, and R is at version 3.4.1. I'd consider updating, this might be the reason for your issues. ...
written 8 days ago by andrew.j.skelton733.7k
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Comment: C: Inserting Noise into RNA-seq raw counts
... Instead of using some existing RNA seq data, try simulating it yourself, you can then control the "noise" by parameterisation. Something like [Polyester][1] should do that. [1]: https://github.com/alyssafrazee/polyester ...
written 8 days ago by andrew.j.skelton733.7k
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Comment: C: Perform differential expression for illumina data
... Can you amend your post with `sessionInfo()` ...
written 8 days ago by andrew.j.skelton733.7k
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Comment: C: Perform differential expression for illumina data
... Try explicit parameterisation: `fit <- limma::lmFit(object = selDataMatrix, design = design)` ...
written 8 days ago by andrew.j.skelton733.7k
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Comment: C: Perform differential expression for illumina data
... Strange, It could be a namespace problem. Try: `fit <- limma::lmFit(selDataMatrix, design)` ...
written 8 days ago by andrew.j.skelton733.7k
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Comment: C: Perform differential expression for illumina data
... Put in the results of: `head(selDataMatrix)` `head(design)` ...
written 8 days ago by andrew.j.skelton733.7k
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Comment: C: Perform differential expression for illumina data
... > I doubt the data is not of correct format Famous last words... It seems from the error you've presented, there's something amiss with your `selDataMatrix` object. Useful commands to try out: - `str(selDataMatrix)` - Structure of your object `dim(selDataMatrix)` - Dimensions of your object ...
written 8 days ago by andrew.j.skelton733.7k
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Comment: C: Salmon never completes, stuck on processing fragments
... Looks like you're running this on your Mac, are you sure you want that many threads? ...
written 10 days ago by andrew.j.skelton733.7k
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Answer: A: retrospective trio analysis from WGS SNPs
... I recently came across [Peddy][1] that I'll be trying out soon. [VCF tools][2] also has a couple of implementations in `--relatedness` and `--relatedness`, which are based on Yang et al, and Manichaikul et al respectively. There's also [KING][3] which I think was used in ExAC. [1]: https://gith ...
written 12 days ago by andrew.j.skelton733.7k

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