Tag: enhancedVolcano

Error in Enhanced Volcano : unused arguments

Hi All, So i an currently attempting to use Enhanced volcano to visualise a set of RNA-seq data, but when I run the below script, I get back the error message below. Does anyone know what the problem is – I can’t see anything wrong in the code. Error in…

Continue Reading Error in Enhanced Volcano : unused arguments

Understanding the output of Negative Binomial in DESeq2

Are zero is a default option of log2fold change to be considered as up and down? Yes, by default, the null hypothesis is that the log2FoldChange is zero. Does this mean that there are seven genes in total that will have significant adjusted p-value? Yes, you are interpreting your results…

Continue Reading Understanding the output of Negative Binomial in DESeq2

Replacing default numbers with geneNames in enhancedVolcano

Replacing default numbers with geneNames in enhancedVolcano 0 Hi Kevin, I am trying to plot a volcano plot with my DESeq2 results. I managed to get it working with most of the files, but I cant get rid of the default row numbers and replace it with geneName. Any help…

Continue Reading Replacing default numbers with geneNames in enhancedVolcano

Volcano plot not centered at origin

I am making a volcano plot for my phosphoproteomics data and seemingly the data are not centered around the origin. The reason that I know there is something wrong is because before my code was producing the correct volcano plot, and now it is shifted. What are some reasons why…

Continue Reading Volcano plot not centered at origin

Bioconductor – DESeq2

DOI: 10.18129/B9.bioc.DESeq2     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: 3.10 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on…

Continue Reading Bioconductor – DESeq2

Bioconductor Forum

James W. MacDonald 57k 1 week, 5 days ago United States Answer: Biomart’s getBM returns no genes for an existing GO-term in grch38, and less the Michael Love 33k 1 week, 6 days ago United States Answer: Normalizing 5′ Nascent RNA-seq data to identify differentially expressed transcr Kevin Blighe 3.3k 2 weeks, 2 days ago Republic…

Continue Reading Bioconductor Forum