User: moldach

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moldach10
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United States
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Posts by moldach

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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 20 days ago by moldach10
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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 20 days ago by moldach10
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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 20 days ago by moldach10
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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 20 days ago by moldach10
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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 20 days ago by moldach10
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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 21 days ago by moldach10
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Using Human Protein Atlas annotations with pRoloc to interpretate subcellular location
... 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 ...
annotation subcellular location proloc written 21 days ago by moldach10 • updated 21 days ago by Laurent Gatto900
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Comment: C: Getting data into (and out of) the MSnSet object
... 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 28 days ago by moldach10
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Answer: A: Getting data into (and out of) the MSnSet object
... 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 4 weeks ago by moldach10
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Comment: C: Getting data into (and out of) the MSnSet object
... Hello and thank you for trying to help me Laurent. I'll put this into two comments for clarity. One thing I wanted to know was how to actually inspect the sample data provided in the pRoloc data set. I'll use hyperLOPIT-SIData-ms3-rep12-intersect.csv since this is what you showed above. I figured ...
written 4 weeks ago by moldach10

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