User: nhejazi

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Posts by nhejazi

<prev • 11 results • page 1 of 2 • next >
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Answer: A: biotmle package error with heatmap/dendrogram
... Please see the answer at https://github.com/nhejazi/biotmle/issues/61. Note that this will be resolved upon the next release of Bioconductor v3.9. ...
written 7 months ago by nhejazi0
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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 2.2 years 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 2.2 years ago by nhejazi0 • updated 2.1 years ago by andrew.blake40
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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 2.4 years 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 2.4 years 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 2.4 years 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 2.8 years 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 2.8 years ago by nhejazi0 • updated 2.8 years ago by Martin Morgan ♦♦ 23k
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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 2.8 years ago by nhejazi0 • updated 2.8 years ago by Michael Lawrence11k
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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 3.1 years ago by nhejazi0 • updated 3.1 years ago by Michael Lawrence11k

Latest awards to nhejazi

Autobiographer 7 months ago, has more than 80 characters in the information field of the user's profile.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For BiocParallel/scater warning after move to R 3.4.0

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