## User: moldach

moldach10
Reputation:
10
Status:
New User
Location:
Website:
https://www.moldach.gi...
@MattOldach
Last seen:
3 days, 13 hours ago
Joined:
4 years ago
Email:
m******@ucalgary.ca

#### Posts by moldach

<prev • 19 results • page 1 of 2 • next >
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... 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 ...
written 5 months ago by moldach10 • updated 5 months ago by Yuan Tian120
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... 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 ...
written 7 months ago by moldach10
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... 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 ...
written 8 months ago by moldach10
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... 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 ...
written 13 months ago by moldach10 • updated 12 months ago by James W. MacDonald51k
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... 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 20 months ago by moldach10
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... 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 20 months ago by moldach10
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... 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 20 months ago by moldach10
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... Thank you for your prompt and detailed reply Laurent. Thanks for clearing up that markers can be selected in a number of ways (e.g. pRolocmarkers, GO CC [with additional curation], HPA, etc.). There are 11 high-confidence marker categories in pRolocmarkers:   > table(pRolocmarkers("hsap")) ...
written 20 months ago by moldach10
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... In the Path2PPI package vignette, section 2.1., the list of proteins associated with the pathway of interest (i.e. "autophagy induction") for yeast and human are provided in two named character vectors “yeast.ai.proteins”  and "human.ai.proteins”.  I found the detail for how one could do this for t ...
written 20 months ago by moldach10
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