Changes between Version 35 and Version 36 of SOPs/rna-seq-diff-expressions

Timestamp:

04/27/17 08:20:51 (8 years ago)

Author:

gbell

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -79 +79 @@
      * As with microarray normalization, be aware of the assumptions of each method and choose the method(s) which are most valid with your experiment.
      * Origin of recommendation for upper-quartile normalization: [[http://www.ncbi.nlm.nih.gov/pubmed/20167110|Bullard et al., 2010]]
-     * See [[http://jura.wi.mit.edu/bio/scripts/R/normalize_DGE_matrix.R|normalize_DGE_matrix.R]] for a command-line script for count normalization
+     * Use DESeq, DESeq2, or see [[http://jura.wi.mit.edu/bio/scripts/R/normalize_DGE_matrix.R|normalize_DGE_matrix.R]] for a command-line script for count normalization
        * Methods for above script: mean, median, quantile, percentile, none
        * Outputs also includes before and after image files: boxplots, scatterpots, violin plots