Changes between Version 2 and Version 3 of SOPs/rna-seq-diff-expressions/EdgeR

Timestamp:

10/31/25 16:48:15 (2 days ago)

Author:

kdesilva

Comment:

--

SOPs/rna-seq-diff-expressions/EdgeR

@@ -10 +10 @@
   * Outputs also includes image files: boxplot, MA plot, volcano plot.
   * Sample command:
-     * ''bsub "R --vanilla < get_DE_genes_with_edgeR.R edgeR_sample_input.txt 2 5 edgeR_sample_output.txt"''
+     * ''sbatch --job-name=edgeR_analysis --wrap="R --vanilla < get_DE_genes_with_edgeR.R edgeR_sample_input.txt 2 5 edgeR_sample_output.txt"''
   * In running edgeR, the parameter //prior.n// should be chosen where the default value is 10.  //prior.n// determines the amount of smoothing tagwise dispersion towards the common dispersion.\\   The suggested method for choosing //prior.n// is to ensure //prior.n * df// is approx 50 where degrees of freedom (df) = lib. size - number of groups.  //prion.n// should generally be greater than 5.  For more details see section 6.4 [[http://bioconductor.org/packages/2.7/bioc/vignettes/edgeR/inst/doc/edgeR.pdf|edgeR Manual]].