Changes between Version 3 and Version 4 of SOPs/diff_rnaSeq


Ignore:
Timestamp:
10/31/25 15:57:28 (3 days ago)
Author:
kdesilva
Comment:

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  • SOPs/diff_rnaSeq

    v3 v4  
    3737  * Outputs also includes image files: boxplot, MA plot, volcano plot
    3838  * Sample command:
    39      * ''bsub "R --vanilla < get_DE_genes_with_edgeR.R edgeR_sample_input.txt 2 5 edgeR_sample_output.txt"''
     39     * ''sbatch --job-name=edgeR_analysis  --wrap="R --vanilla < get_DE_genes_with_edgeR.R edgeR_sample_input.txt 2 5 edgeR_sample_output.txt"''
    4040  * 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]]
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