User: moldach

gravatar for moldach
moldach10
Reputation:
10
Status:
New User
Location:
Canada/Montreal/Douglas Mental Health Institute
Website:
https://www.moldach.gi...
Twitter:
@MattOldach
Last seen:
3 weeks, 4 days ago
Joined:
3 years, 10 months ago
Email:
m******@ucalgary.ca

Posts by moldach

<prev • 19 results • page 1 of 2 • next >
0
votes
1
answer
98
views
1
answer
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 10 weeks ago by moldach10 • updated 10 weeks ago by Yuan Tian110
0
votes
0
answers
63
views
0
answers
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 4 months ago by moldach10
0
votes
0
answers
156
views
0
answers
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 5 months ago by moldach10
1
vote
1
answer
315
views
1
answer
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 10 months ago by moldach10 • updated 10 months ago by James W. MacDonald50k
0
votes
1
answer
373
views
1
answers
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 17 months ago by moldach10
0
votes
1
answer
373
views
1
answers
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 17 months ago by moldach10
1
vote
1
answer
314
views
1
answers
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 17 months ago by moldach10
0
votes
1
answer
314
views
1
answers
Comment: C: Using Human Protein Atlas annotations with pRoloc to interpretate subcellular lo
... 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 17 months ago by moldach10
0
votes
0
answers
248
views
0
answers
How to get proteins which are associated with a specific pathway of interest and subset iRefIndex files which contain the relevant interactions
... 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 ...
path2ppi written 17 months ago by moldach10
0
votes
1
answer
373
views
1
answer
Trouble using addMarkers from pRoloc on my own dataset
... I'm having trouble adapting the pRoloc vignette to my own data set; specifically section 2.4 "pRoloc's organelle markers". The vignette tell you to see ?addMarkers in R in order to add these to a new MSnSet class object. First you need to specify the parameters for the available marker set obtaine ...
proteomics msnset proloc written 17 months ago by moldach10

Latest awards to moldach


Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 330 users visited in the last hour