User: moldach

gravatar for moldach
moldach20
Reputation:
20
Status:
New User
Location:
Canada/Montreal/Douglas Mental Health Institute
Website:
https://www.moldach.gi...
Twitter:
@MattOldach
Last seen:
1 week, 5 days ago
Joined:
4 years, 3 months ago
Email:
m******@ucalgary.ca

Posts by moldach

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Error: no applicable method for `RunTSNE` applied to an object of class "try-err
... Hi Martin, I didn't realize Seurat wasn't under the Bioconductor umbrella and apologize for not including a `reprex` - I've done so now. Thank you very much for providing a very helpful answer anyways! ``` library(dplyr) library(Seurat) library(tibble) # Download ~11Mb file - subset from SRA653 ...
written 5 weeks ago by moldach20
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Error: no applicable method for `RunTSNE` applied to an object of class "try-error"
... I'm running into issues trying to catch errors thrown from `Seurat::RunTSNE()` inside of a function. When users input a small dataset we've noticed that this function will fail with the error: > Error in .check_tsne_params(nrow(X), dims = dims, perplexity = perplexity, : perplexity is too la ...
scrna seurat debugging exceptions unit-test written 5 weeks ago by moldach20 • updated 5 weeks ago by Martin Morgan ♦♦ 24k
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could not find function "plotQC" in scater package
... When I install the `scater` package it's not bringing in the `plotQC()` function. I get this error: ``` library(scater) scater::plotQC() ``` > could not find function "plotQC" This is my `sessionInfo()`: ``` R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: ...
scater written 7 weeks ago by moldach20 • updated 7 weeks ago by Aaron Lun25k
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ChAMP::champ.norm Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(beta)[x], : task 1 failed - "only defined on a data frame with all numeric variables"
... We've ran into a problem where `ChAMP::champ.norm()` has all of a sudden stopped working for our users. We've ran it again on datasets which have worked previously (on both dfs and matrices) and were getting the same error: ``` test_betas <- data.frame(slide1 = c(0.83930246, 0.81656241, 0.885922 ...
champ methylation bmiq written 7 months ago by moldach20 • updated 7 months ago by Yuan Tian120
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Error for ENmix::bmiq.mc() on one sample
... I've noticed there is a bug when tying to run one sample on `ENmix::bmiq.mc()` and wanted to make a pull request. As this project lives on Bioconductor and not Github not sure the best way to do this (your repo says to fill bug reports here). > Error in 1:ncol(beta.b1) : argument of length 0 Ad ...
enmix written 9 months ago by moldach20
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Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
... I'm getting a rather cryptic error from the `ENmix` package's `bmiq.mc()` function: > Error in ENmix::bmiq.mc(forDNAm_preprocess2, nCores = 2) : BMIQ estimates encountered error, try to run it again I've narrowed the problem down over the past couple of weeks and getting closer to the issu ...
watermelon methylation enmix bmiq written 10 months ago by moldach20
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Minfi read.metharray.sheet error
... I'm having trouble with the minfi package, specifically the read.metharray.sheet function. The missmethyl package vignette loads the sample sheet from minfiData package like so: library(minfi) library(minfiData) baseDir <- system.file("extdata", package = "minfiData") targets <- read.methar ...
dataimport minfi minfidata methylation missmethyl written 15 months ago by moldach20 • updated 15 months ago by James W. MacDonald52k
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Comment: C: Trouble using addMarkers from pRoloc on my own dataset
... I'm also trying to make sense of the plot2D I get with my data. >f <- "https://gist.githubusercontent.com/moldach/446852fcfa1adbb3be2ac754dc616421/raw/42f31e88f38afb7243d61dc46e2321e3ebfdae18/pRoloc-data" >e <- readMSnSet2(f, ecol = 2:20, sep = "\t") >hsap <- pRolocmarkers("hsap" ...
written 22 months ago by moldach20
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Comment: C: Trouble using addMarkers from pRoloc on my own dataset
... I used clusterProfiler to give Uniprot identifiers to my HGNC gene symbols. # Working back from the data I provided just to show the original genes I had - there were only 6538 unique genes f <- read.csv("https://gist.githubusercontent.com/moldach/446852fcfa1adbb3be2ac754dc616421/raw/42f31e88f ...
written 22 months ago by moldach20
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Comment: C: Using Human Protein Atlas annotations with pRoloc to interpretate subcellular lo
... My decision on whether I should use multi-localizing markers for my biological question: From Gatto et al., 2014 "Although proteins with genuine multiple localizations are of particular interest (see below), one must be careful when assessing multiple GO CC terms and distinguish proteins present in ...
written 22 months ago by moldach20

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