User: ivanarg2

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ivanarg260
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Posts by ivanarg2

<prev • 15 results • page 1 of 2 • next >
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Comment: C: ssGSEA 2.0 R Package?
... Got it. I thought the CLI was meant to be used with RStudio commands, but I see that I misinterpreted that. I'll give your advice a shot, and if it doesn't work I'll go back to the original GSVA function and figure out the core issue. Thx for the tips. ...
written 15 days ago by ivanarg260
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Comment: C: ssGSEA 2.0 R Package?
... *Note: the GUI version works, but I can't use RStudio commands to do a batch of 20 analyses* ...
written 15 days ago by ivanarg260
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Comment: C: ssGSEA 2.0 R Package?
... You're probably right, but it's worth a shot. Regarding GitHub, I tried following their instructions, but given that I've never used GitHub before, and that I only use packages from CRAN/BioConductor, I don't know how to implement their instructions. Currently, I'm getting the following error when I ...
written 15 days ago by ivanarg260
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ssGSEA 2.0 R Package?
... Hi all. I've recently ran into some trouble using the GSVA package for running ssGSEA (i.e., gsva(data, pathways, method = 'ssGSEA'). Googling a bit revealed a new ssGSEA 2.0 provided by Broad under their Gene Pattern module (see https://github.com/broadinstitute/ssGSEA2.0 and https://gsea-msigdb.g ...
ssgsea R written 15 days ago by ivanarg260
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Comment: C: RNASeq user experience with Novogene?
... Thanks for your feedback. I'm assuming you're speaking from personal experience, or from colleague's experience right? The website and the data they provide seems pretty good, but I'm wondering if someone here actually worked with them. (It sounds like you did). And yeah, I'm planning to do a stand ...
written 2.1 years ago by ivanarg260
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Forum: RNASeq user experience with Novogene?
... Hi, I'm considering doing RNASeq for the first time on patient samples, and a company called Novogene is offering a really cheap price for RNASeq (1/3 of the cost at my institution's Core). Does anyone have experience with this company? Why is their price so cheap? Should I be concerned about data ...
forum rna-seq written 2.1 years ago by ivanarg260 • updated 5 weeks ago by sapuizait0
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Comment: C: how to find metabolites
... The fgsea package has a few good functions for plotting the results of fgsea analysis ...
written 2.1 years ago by ivanarg260
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Comment: C: how to find metabolites
... I edited my answer based on your edit. ...
written 2.1 years ago by ivanarg260
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Comment: C: how to find metabolites
... To run GSEA you need a vector with (i) gene names, as you provide, and (ii) some kind of ranking variable, like a fold change, a p value, or something like that. Do you have this info from your differential expression analysis? ...
written 2.1 years ago by ivanarg260
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Comment: C: how to find metabolites
... Right. So you already have the two necessary parameters to run GSEA: (i) a list of gene sets (which usually refers to a biological pathway and the genes associated with those pathways, but in this case the gene sets refer to metabolites, and the genes involved in their metabolism); and (ii) a rankin ...
written 2.1 years ago by ivanarg260

Latest awards to ivanarg2

Popular Question 14 months ago, created a question with more than 1,000 views. For RNASeq user experience with Novogene?
Scholar 2.1 years ago, created an answer that has been accepted. For A: how to find metabolites
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: how to find metabolites

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