## User: moldach

moldach10
Reputation:
10
Status:
New User
Location:
United States
Last seen:
3 months, 2 weeks ago
Joined:
3 years, 4 months ago
Email:
m******@ucalgary.ca

#### Posts by moldach

<prev • 16 results • page 1 of 2 • next >
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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 4 months ago by moldach10 • updated 4 months ago by James W. MacDonald49k
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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 11 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 11 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 11 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 11 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 11 months ago by moldach10
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... 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 ...
written 11 months ago by moldach10
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... As my understanding the package pRoloc allows one to study the localisation of protein inside cells , using relative quantitation of known organelle residents, termed organelle markers. In the the vignette it uses tan2009r1 data of markers that have been obtained by mining the pRolocdata datasets ...
written 11 months ago by moldach10 • updated 11 months ago by Laurent Gatto1.1k
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... Thank you very much, exprs(res) <- round(exprs(res) * 1000) appears to work although I'm not exactly sure why? To be clear my data is normalized spectral counts (i.e. NSAF) prior to multiplication by 1000 and rounding. Is that the correct data format to be inputting? ...
written 12 months ago by moldach10
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... So the example from the msmsTests vignette for how to do differential expression analysis with edgeR goes like this: ## Example library(msmsTests) data(msms.dataset) e <- pp.msms.data(msms.dataset) e null.f <- "y~batch" alt.f <- "y~treat+batch" div <- apply(exprs(e),2,sum) res <- ms ...
written 12 months ago by moldach10

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