User: chris86
chris86 • 290
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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 5 weeks ago by
chris86 • 290
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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 3 months ago by
chris86 • 290
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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 4 months ago by
chris86 • 290
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Comment:
A: TopHat mapping error
... Yeah you might use HISAT2 or STAR instead of Tophat. ...
written 6 months ago by
chris86 • 290
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... OK thanks, seems like a nice alternative to cuffmerge etc. ...
written 6 months ago by
chris86 • 290
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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 6 months ago by
chris86 • 290
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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 6 months ago by
chris86 • 290
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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 6 months ago by
chris86 • 290
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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 6 months ago by
chris86 • 290
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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 7 months ago by
chris86 • 290
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