User: stewart999

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stewart99910
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Posts by stewart999

<prev • 4 results • page 1 of 1 • next >
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minfi - error when reading idat files
... Hi I am reading 1000 EPIC samples using minfi's read.metharray.exp() function as follows: RGset <- read.metharray.exp(base=NULL, targets=targets, verbose=TRUE, extended=TRUE) The error I receive at the end of this process is: ... [read.metharray] Creating data matrices ... Error in read.met ...
minfi methylation written 5 months ago by stewart99910 • updated 5 months ago by Kasper Daniel Hansen6.3k
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Is there any way to parallelise sva functions?
... I'm looking to parallelise 2 sva functions: num.sv: where B=20 indicates 20 permutations num.sv(dat, mod, method="be", vfilter=NULL, B=20, seed=NULL) sva: where B=5 is the no. iterations of the irw algorithm sva(dat, mod, mod0=NULL, n.sv=NULL, controls=NULL, method="irw", vfilter=NULL, B=5, nu ...
sva methylation written 7 months ago by stewart99910
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How to convert GenomicRatioSet to RGChannelSet in minfi::compartments()
... I am trying to estimate A/B compartments using minfi's compartments function. The data I have is from whole blood samples, so I want to correct for cellular heterogeneity first. I have done this using minfi's estimateCellCounts function with the option returnAll = TRUE. This returns data corrected ...
minfi methylation estimatecellcounts written 7 months ago by stewart99910 • updated 7 months ago by Kasper Daniel Hansen6.3k
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Can't install 'lumi'
... I've compiled and installed R-3.3.2 but can't install lumi   I'm not sure if lumi is still in development or if it's not properly indexed in bioconductor as the release page for lumi (https://www.bioconductor.org/packages/release/bioc/html/lumi.html) has the string "Bioconductor version: Developme ...
lumi written 13 months ago by stewart99910 • updated 13 months ago by Martin Morgan ♦♦ 21k

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