Differentail gene expression results
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5 weeks ago

can anyone suggest me about the results of differential gene expression analysis using DESeq2. i have 10 samples, of which 6 are disease and 4 are healthy, i have find the raw counts and now i have run the following code on my data . Note" i have't collapse/merge the samples" the R script

the output results of this is output of DESeq2

differential expression gene rna-seq Deseq2 • 300 views
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What is your question?

See https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html which covers most relevant aspects for beginners.

General notes:

  • your prefilter (keep) is basically not doing anything relevant other than removing genes that are only zero, see the vignette on prefilters
  • do some basic QC, for example PCA; see vignette
  • plot results, e.g. MA-plots, see vignette
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