User: koneill

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koneill30
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Canada
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1 month, 2 weeks ago
Joined:
2 years, 6 months ago
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k******@bccrc.ca

Posts by koneill

<prev • 7 results • page 1 of 1 • next >
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Answer: A: flowBin: error when calculating medianFIDist
... You're welcome! Re: transformations, in general before further analysis you should be doing some preprocessing, including compensation (if that hasn't been applied), some kind of logarithmic transformation (logicle/biexponential is the preferred/FlowJo option), normalisation (optional), gating for ...
written 9 weeks ago by koneill30
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Answer: A: flowBin: error when calculating medianFIDist
... Hi Kelly! Thanks for digging deep into the code base to find this. Yes, having linear data is likely to be the problem -- R turns very large numbers into "Inf".  The assumption there is a log10 transformation may be a bit of a leap, but this is the most common case in flow data (or, rather, that ...
written 9 weeks ago by koneill30
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Answer: A: Plotting the results of flowType
... Unfortunately selecting markers isn't supported in the plot function in flowType right now. But you can do this manually using some of flowType's helper functions. This would also give you more control over the plotting:   ################################################### ### code chunk number ...
written 11 months ago by koneill30
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Answer: A: bigBed support in rtracklayer
... I guess this never went further? I see there is bigBed.h in the UCSC source in the rtracklayer package, but there doesn't seem to be actual bigBed functionality exposed at the R level. For now, loading in bigBed to R seems to be impossible, and the only solution for working with bigBed files is to ...
written 18 months ago by koneill30
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Comment: C: export.bw produces enormous files (10^5 times bigger than they should be)
... Thanks, Michael! ...
written 22 months ago by koneill30
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export.bw produces enormous files (10^5 times bigger than they should be)
... Hi I was trying to write out some tracks of averaged methylation data (represented as GenomicRanges objects) as bigWig files using export.bw, but for my simple 1Mbp window data (2,700 ranges), it produced a 2GB file! Testing with the not-run example in the documentation, this holds as well. The ex ...
rtracklayer bigwig written 22 months ago by koneill30 • updated 22 months ago by laurent.lacroix0
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Answer: A: flowType 2.6.0 vs flowType 2.4.0
... Hi Pat, Kieran here, the other author/maintainer of flowType. The issue is a silly case-sensitivity issue: at the moment, the code wants you to specify Methods='Thresholds', not Methods='thresholds' (contrary to what the documentation says). I could have sworn I'd fixed this a long time ago! Anywa ...
written 2.5 years ago by koneill30

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