User: nhejazi

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nhejazi0
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Posts by nhejazi

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Comment: C: BiocParallel/scater warning after move to R 3.4.0
... Just thought I'd note here that, at least in my case, updating from Bioconductor 3.4 to 3.5 (with BiocInstaller 1.26.0), and then updating all packages via `biocLite()`, fixed this issue. I had to uninstall and then re-install "BiocInstaller", as noted on the Bioconductor webpage for using the "Deve ...
written 6 months ago by nhejazi0
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BiocParallel/scater warning after move to R 3.4.0
... After the recent update to R 3.4.0, updates and installation of several Bioconductor packages return a warning during installation -- specifically, there seems to be an issue in how BiocParallel sets up its core classes: Warning in is.na(x[[i]]) : is.na() applied to non-(list or vector) of type ...
biocparallel scater written 6 months ago by nhejazi0 • updated 4 months ago by andrew.blake10
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Comment: C: minfi "mapToGenome" dimension error
... It looks like the update fixed everything, at least related to the use of `minfi::mapToGenome`. Thanks for your help, Kasper! ...
written 8 months ago by nhejazi0
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Comment: C: minfi "mapToGenome" dimension error
... Thanks for your quick reply, Kasper. I've added the information produced by "traceback()" and "biocValid()" (it seems like the latter of these includes the same information produced by "sessionInfo()"). ...
written 8 months ago by nhejazi0
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minfi "mapToGenome" dimension error
... I have recently begun using `minfi` for the analysis of 850K methylation data from the Illumina EPIC array. In following a fairly standard procedure (as in the the 2014 Bioconductor tutorial on using minfi for 450K data), I've encountered the following error, which arises anytime that `mapToGenome` ...
minfi methylation epic microarray methylationepic written 8 months ago by nhejazi0
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Comment: C: Operations across Lists of GenomicRanges?
... The premise is simply that a particular data analytic function (e.g., limma) is called on a data set in data.frame or GenomicRanges form. The output is a data structure of genomic sites or regions (e.g., seqnames, positions, etc.). The list returned by foreach contains 1000+ of such output tables. T ...
written 13 months ago by nhejazi0
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Comment: C: Operations across Lists of GenomicRanges?
... Example Code: permute_limma <- foreach (i = 1:nsim) %dopar% { set.seed(6401^2) design_2 <- sample(design) print(paste0("Limma - the ", i, "th iteration is underway.")) fit <- lmFit(y, design_2) fit <- eBayes(fit) tt <- topTable(fit, coef = 2,adjust.method = " ...
written 13 months ago by nhejazi0 • updated 13 months ago by Martin Morgan ♦♦ 20k
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Operations across Lists of GenomicRanges?
... I am currently working with GenomicRanges structures stored in a large list (~10,000 entries) produced via output from a `foreach` loop. These lists all contain similar GenomicRanges structures, and I would like to generate a single GenomicRanges or data.frame structure with all of the unique entrie ...
genomicranges plyr lists written 13 months ago by nhejazi0 • updated 13 months ago by Michael Lawrence9.8k
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Collapse/Reduce in GRanges by Metadata Column
... I've only recently adopted GRanges for problems like the one below; my apologies in advance if this or similar questions have been answered many times already (I couldn't find anything in various searches...) I have a GRanges structure like the one below. Using values in the metadata column X, I'd ...
granges merge reduce written 16 months ago by nhejazi0 • updated 16 months ago by Michael Lawrence9.8k
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Bounded Regression with Limma for RRBS?
... Main Question: I have been working on an analysis of RRBS data, using various utility function to generate a data matrix that consists of averages of proportions of methylated reads at a list of CpG islands for each of the n = 59 subjects (the dimension of the matrix is roughly 15,000 x 59). The `l ...
limma bsseq rrbs written 17 months ago by nhejazi0 • updated 17 months ago by Aaron Lun17k

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