Question: MD Plot with Glimma starting from DESeq2 results
gravatar for daniele.ottaviani.88
12 months ago by
daniele.ottaviani.880 wrote:


I'm trying to visualize results from the DESeq2 pepeline in interactive html, useing Glimma.

I read the vignette at "glMDPlot.DESeqResults" but I can't understand where to find the "counts", "anno" and "groups" arguments in the DESeqResults object (I made the DESeqDataSet starting from a FeatureCounts matrix of count and a .csv table for metadata). All the MDPlots examples I found so far can call arguments from SummarizeExperiment... but the Glimma vignette's claimig it's possible to start from DESeq2 too. I'm sure I'm missing something easy, but someone might can give me an example of this MD visualization of DESeq2 results, starting from a featurecount matrix and table of metadata?

Here following the code from the Glimma vignette:

**# S3 method for class DESeqResults**
glMDPlot(x, counts, anno, groups, ....)
x = the DESeqResults object.
counts = the matrix of expression values, with samples in columns.
anno = the data.frame containing gene annotations.
groups = the factor containing experimental groups of the samples.

Many Thanks in advance.


rna-seq glimma deseq2 • 504 views
ADD COMMENTlink modified 12 months ago by Jennifer Hillman Jackson25k • written 12 months ago by daniele.ottaviani.880
gravatar for Jennifer Hillman Jackson
12 months ago by
United States
Jennifer Hillman Jackson25k wrote:


This is the Bioconductor tutorial you are using?

If so, asking this question at their support site is what they recommended (this support site is for Galaxy usage).

If you want to try or learn how to use DeSeq2 in Galaxy, please see our tutorials here:

Hope they can help! Jen, Galaxy team

ADD COMMENTlink modified 12 months ago • written 12 months ago by Jennifer Hillman Jackson25k
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