Changes between Version 1 and Version 2 of SOPs/rna-seq-diff-expressions/EdgeR

Timestamp:

01/25/13 09:47:26 (12 years ago)

Author:

gbell

Comment:

--

SOPs/rna-seq-diff-expressions/EdgeR

@@ -6 +6 @@
   * Input for edgeR should be a matrix of counts, not RPKM values.
     * From the edgeR manual: "RPKM values should not be used for assessing differential expression of genes between samples in edgeR. We use the raw counts, because the methods implemented in edgeR are based on the negative binomial distribution, a discrete distribution."
-  * See [[http://iona.wi.mit.edu/bio/bioinfo/Rscripts/get_DE_genes_with_edgeR.R|get_DE_genes_with_edgeR.R]] for a command-line script to use edgeR.
+  * See [[http://jura.wi.mit.edu/bio/scripts/R/get_DE_genes_with_edgeR.R|get_DE_genes_with_edgeR.R]] for a command-line script to use edgeR.
   * Major edgeR upgrade (April 2010?) required a change from version 0.1 to 0.2 of above script.
   * Outputs also includes image files: boxplot, MA plot, volcano plot.