User: restonpiston

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restonpiston20
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Posts by restonpiston

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Suggestions for avoiding False Positives while identifying differentially expres
... First of all, it is not advisable to check for DEG between the replicates themselves, unless you have a very good reason for it (you know one of them were treated differently, etc.). I would also advice that you limit your efforts to comparisons between the categories, as they will provide more mean ...
written 12 days ago by restonpiston20
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Comment: C: GO enrichment tools
... Hello restonpiston! We believe that this post does not fit the main topic of this site. Found a tool that suited my needs For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in ...
written 12 days ago by restonpiston20
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Comment: C: GO enrichment tools
... I checked it out, very nice tool, what I needed to be honest! The only disadvantage is that I had to unravel the obo file to annotate the genes also to the ancestors, but after doing so I could test enrichment and gene set quite easily. ...
written 13 days ago by restonpiston20
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Comment: C: GO enrichment tools
... I have updated my answer, I was not very specific, you are right ...
written 16 days ago by restonpiston20
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(Closed) GO enrichment tools
... Hello everyone! I have recently started to analyze RNA-seq data and I would like to know which tools are current now for the purpose of GO enrichment. I have checked out topGO, BiNGO, and building my own hypergeometric test, but none really satisfied me. I am looking for suggestions of tools that ...
R rna-seq go written 16 days ago by restonpiston20 • updated 16 days ago by EagleEye6.4k
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Answer: A: GeneId to GO terms
... First you have to download the GAF file corresponding to your species from [here][1] Then you can run this small script to get the GO terms you are looking for. data<-read.delim(file="input/sgd.gaf",sep = "\t", as.is=TRUE, header=FALSE, comment.char="!") data<-data[,c("V5","V9","V11" ...
written 18 days ago by restonpiston20
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Answer: A: Interpreting GSEA enrichment plots/results
... I was in your position a few weeks ago, and I found [this link][1] from GSEA in the generated report. The peak point of the green plot is your ES (enrichment score), which tells you how over or under expressed is your gene respect to the ranked list. The second part of the graph (middle with red ...
written 19 days ago by restonpiston20
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Comment: C: GSEA Tool to use with RNA-seq data
... Thanks for the answer! I have managed to use it and it works pretty well, even tho I had to modify my data a bit, as I am using custom pathway annotations. ...
written 19 days ago by restonpiston20
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Comment: C: GSEA Tool to use with RNA-seq data
... Thanks for the answer! Unfortunately, I do not seem to be able to have it working. I have input the data like this: ![WebGestalt Saccharomyces][1] Maybe you could tell me what I am doing wrong? I am receiving "R error (1565083554)". [1]: https://i.imgur.com/wBYMnQA.png ...
written 19 days ago by restonpiston20
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GSEA Tool to use with RNA-seq data
... Hello, I'm working with a set of RNA-seq data which I want to analyze the Gene Ontolgy Enrichment and the metabolic pathways from Kegg. I have already checked the Pathways and the GO using the hypergeometric test, but I wanted to cross check the results using the Gene Set Enrichment. Optimally I w ...
rna-seq gsea written 20 days ago by restonpiston20 • updated 20 days ago by Buffo1.6k

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