User: chris86
chris86 • 330
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- https://intobioinforma...
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I am a post-doc data analyst working in London in stratified medicine.
Posts by chris86
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... This is what you want: https://github.com/dswatson/bioplotr/blob/master/R/plot_drivers.R.
I suggest everyone check out this function for assessing the drivers of variation, it requires installation of David Watsons bioplotr package. ...
written 6 months ago by
chris86 • 330
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Comment:
C: pre-filtering expression data
... Aside from removing features that are not expressed at all (simple R commands to do that are easy to find), you can filter based on variance or median absolute deviation. For instance, the M3C package includes a function to do this, you can see section 5.2 of the package vignette (https://bioconduct ...
written 9 months ago by
chris86 • 330
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... At least from a clustering perspective, I'd probably try it both ways to be on the safe side, i.e. with PCA to get the top N PCs and without. I'm a bit skeptical of reducing to N PCs for clustering because there is inevitable information loss. The same will apply for t-SNE, UMAP, etc. I'd prefer to ...
written 10 months ago by
chris86 • 330
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Comment:
A: TopHat mapping error
... Yeah you might use HISAT2 or STAR instead of Tophat. ...
written 12 months ago by
chris86 • 330
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... OK thanks, seems like a nice alternative to cuffmerge etc. ...
written 12 months ago by
chris86 • 330
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... Andrew, what is the best way to annotate my taco transcripts using my human reference .gtf? Like I need a gene ID and symbol for each one. I could use the co-ordinates and write a script, but what do you do? ...
written 12 months ago by
chris86 • 330
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... This is a good point, surely duplicating the transcriptome is going to screw up quantification of transcripts and differential expression downstream? Did you find an answer to this? ...
written 12 months ago by
chris86 • 330
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... I see. That is also interesting about ballgown.
I like your package btw, but the vignette and manual are full of many spelling errors you should correct. ...
written 12 months ago by
chris86 • 330
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... Kristoffer, can I ask why you don't mention Sleuth and Ballgown which, as far as I understand, were developed for a transcript based differential expression analysis starting with transcript quantifications? Thanks. ...
written 12 months ago by
chris86 • 330
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... I wouldn't bother consensus clustering with really small sample sizes like that because your statistical power is poor, IMO better to use standard hierarchical clustering with aheatmap or complexheatmap.
I usually consensus cluster with large samples sizes like at least over 60. I think the resampl ...
written 12 months ago by
chris86 • 330
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