User: andrew.j.skelton73
andrew.j.skelton73 • 3.7k
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Posts by andrew.j.skelton73
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... 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.skelton73 • 3.7k
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... 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.skelton73 • 3.7k
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... 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.skelton73 • 3.7k
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... Can you amend your post with `sessionInfo()` ...
written 8 days ago by
andrew.j.skelton73 • 3.7k
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... Try explicit parameterisation: `fit <- limma::lmFit(object = selDataMatrix, design = design)` ...
written 8 days ago by
andrew.j.skelton73 • 3.7k
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... Strange, It could be a namespace problem. Try: `fit <- limma::lmFit(selDataMatrix, design)` ...
written 8 days ago by
andrew.j.skelton73 • 3.7k
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... Put in the results of:
`head(selDataMatrix)`
`head(design)` ...
written 8 days ago by
andrew.j.skelton73 • 3.7k
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... > 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.skelton73 • 3.7k
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... Looks like you're running this on your Mac, are you sure you want that many threads? ...
written 10 days ago by
andrew.j.skelton73 • 3.7k
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... 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.skelton73 • 3.7k
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