Question: DESeq2 workflow for RNAseq
gravatar for Ambika
2.7 years ago by
United States
Ambika30 wrote:

Hi everyone,

I just made some graphics Pheatmap and MA plot using DESeq2 for my RNAseq differential expression analysis. However now I am really confused on what to do next. Can I make some table and calculate number of expressed genes across samples. If I could compare the data for my replications and treatments through barplots and venndiagrams .I tried to look on so many stuffs which is just making me more confused.

Looking forward for the suggestions and guidelines.

Thank you,


rna-seq • 1.6k views
ADD COMMENTlink modified 2.7 years ago by Devon Ryan95k • written 2.7 years ago by Ambika30
gravatar for Devon Ryan
2.7 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k wrote:

You can plot the (normalized) counts across your samples for particular genes if you'd like. However, looking for "expressed" genes that change between samples is usually not useful (there's no really useful definition of "expressed"). Normally one takes the statistical results from DESeq2 and then goes from there, with things like GO/pathway enrichment or simply looking at what the various DE genes are.

ADD COMMENTlink written 2.7 years ago by Devon Ryan95k

Devon Ryan thank you for the clarification. I think I will just be looking at what DE genes are. So in order to plot the counts across my samples how can I write a table for transformed values?

Thank you, Ambika

ADD REPLYlink written 2.7 years ago by Ambika30

Just use the plotCounts() function.

ADD REPLYlink written 2.7 years ago by Devon Ryan95k

C: Using DESeq2 results for building a classifier

What are your thoughts? You reckon I should use an independent set of samples to check for accuracy?

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Uday Rangaswamy120

That would be fine and it would be better to post questions like this as standalone posts.

ADD REPLYlink written 2.3 years ago by Devon Ryan95k
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