Changes between Version 49 and Version 50 of SOPs/rna-seq-diff-expressions

Timestamp:

06/20/17 12:17:24 (8 years ago)

Author:

gbell

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -99 +99 @@
     * Method 2: Use the fpkm() function from DESeq2.  This method requires raw counts and any measure of gene length (such as mean or median length of transcripts of gene) that one needs to produce independently (or create a GRanges data structure).  It can produce (raw) FPKMs [using fpkm(... robust = FALSE)] and normalized FPKMs [using fpkm(... robust = TRUE)].
 
-    * Method 3: Using Cuffquant to get '''normalized''' FPKMs, as described with [http://cole-trapnell-lab.github.io/monocle-release/getting-started/ monocle] and [http://cole-trapnell-lab.github.io/cufflinks/cuffnorm/#running-cuffnorm Cuffnorm]. The default normalization for Cuffnorm is the same than the normalization performed by DESeq.
+    * Method 3: Use Cuffquant to get '''normalized''' FPKMs, as described with [http://cole-trapnell-lab.github.io/monocle-release/getting-started/ monocle] and [http://cole-trapnell-lab.github.io/cufflinks/cuffnorm/#running-cuffnorm Cuffnorm]. The default normalization for Cuffnorm is the same as the normalization performed by DESeq.
 
     * Method 4: Use featureCounts