User: cado

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cado0
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Posts by cado

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Histogram plot of padj values
... Hi, I'm carrying out DE analysis on RNASeq data in DESeq2. I have a question about the histogram plots I used to plot the p-adj values of my results. I'm referring to this post; http://varianceexplained.org/statistics/interpreting-pvalue-histogram/ to best explain my histogram plots! I have two s ...
rna-seq histograms statistics written 9 months ago by cado0 • updated 9 months ago by RamRS27k
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Comment: C: Pathway Analysis Help
... What format are the geneIDS in geneList of the package DOSE that they use as an example in clusterProfiler? e.g: head(names(geneList)) [1] "4312" "8318" "10874" "55143" "55388" "991" . Also if I'm using clusterProfiler for visualisations is that redoing the GO analysis I've already done in PANTHE ...
written 10 months ago by cado0
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Comment: C: Pathway Analysis Help
... Yes protein families, biological processes and pathways are what I would expect given my experimental conditions. I want to represent this data clearly now. Is pathview in R a good package for this? ...
written 10 months ago by cado0
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Pathway Analysis Help
... Hi, I'm a newbie to bioinformatics so apologies for the naivety of my question. I'm doing RNASeq analysis on a list of genes (bacterial genome) under one condition vs another. After using the DESeq2 package in R, I have a list of up+downregulated DE genes. I did gene enrichment analysis on them usi ...
gene rna-seq written 10 months ago by cado0

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