User: ivanarg2

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ivanarg240
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Posts by ivanarg2

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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 4 months ago by ivanarg240
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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 4 months ago by ivanarg240 • updated 4 months ago by Eric Lim1.1k
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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 4 months ago by ivanarg240
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Comment: C: how to find metabolites
... I edited my answer based on your edit. ...
written 4 months ago by ivanarg240
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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 4 months ago by ivanarg240
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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 4 months ago by ivanarg240
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Comment: C: how to find metabolites
... You can then run regular gene set enrichment analysis, as below: fgsea(metabolites.gs, ranks, nperm = 1000) ## ranks is from your differential expression analysis, i.e., a t-statistic (logFC/logFC.sd) The resulting list of 'pathways' (really, metabolites), will tell you the enrichment of metab ...
written 4 months ago by ivanarg240
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Answer: A: how to find metabolites
... Based on this, with some modifications: > https://support.bioconductor.org/p/107927/ library(KEGGREST) library(org.Hs.eg.db) library(annotate) ## Get enzyme-gene annotations res1 = keggLink("enzyme", "hsa") tmpDF1 = data.frame(ec = res1, gene = names(res1)) ...
written 5 months ago by ivanarg240
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Answer: A: breast cancer transcriptome
... Use the Xena Browser, selected TCGA BRCA, select "Phenotype" and the "sample_type" will give you tumor and normal data. You can play with the heatmaps as well as download the data. https://xenabrowser.net/heatmap/ ...
written 5 months ago by ivanarg240
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Comment: C: how to find metabolites
... Check section 4.5.2 here: https://bioconductor.org/packages/release/bioc/vignettes/piano/inst/doc/piano-vignette.pdf and reference 6 therein. They describe making 'gene sets' where each gene set is a metabolite, and the genes within each set are the enzymes related to metabolism of that metabolite. ...
written 5 months ago by ivanarg240

Latest awards to ivanarg2

Scholar 4 months ago, created an answer that has been accepted. For A: how to find metabolites
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: how to find metabolites

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