Changes between Version 20 and Version 21 of SOPs/rna-seq-diff-expressions

Timestamp:

09/11/14 15:57:37 (10 years ago)

Author:

gbell

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -96 +96 @@
     * Some statistical tests or packages can be applied to non-replicated data (but must be interpreted with a high degree of caution):
        * [[http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff|cuffDiff]] (part of the cufflinks package; uses BAM files as input)
-       * [[http://www.bioconductor.org/packages/release/bioc/html/DESeq.html|DESeq]] [wiki:SOPs/rna-seq-diff-expressions/DESeq | More detail about DESeq]  (This is our preferred method.)
+       * [[http://www.bioconductor.org/packages/release/bioc/html/DESeq.html|DESeq]] [wiki:SOPs/rna-seq-diff-expressions/DESeq | More detail about DESeq]
        * [[http://bioinfo.cipf.es/noiseq/doku.php?id=tutorial|NOISeq]] [wiki:SOPs/rna-seq-diff-expressions/NOISeq | More detail about NOISeq]
        * Fisher's exact test (with R and/or with BaRC R script) [wiki:SOPs/rna-seq-diff-expressions/Fisher | More detail about Fisher's exact test]
     * Some statistical tests or packages are designed for experiments with replication:
-      * [[http://www.bioconductor.org/packages/release/bioc/html/DESeq.html|DESeq]]  [wiki:SOPs/rna-seq-diff-expressions/DESeq | More detail about DESeq]
+      * [[http://www.bioconductor.org/packages/release/bioc/html/DESeq.html|DESeq]]  [wiki:SOPs/rna-seq-diff-expressions/DESeq | More detail about DESeq]    (This is our preferred method.)
+      * [[http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html|DESeq2]]  (We haven't compared this with DESeq very thoroughly.)
       * [[http://www.bioconductor.org/packages/release/bioc/html/edgeR.html|edgeR]]  [wiki:SOPs/rna-seq-diff-expressions/EdgeR | More detail about EdgeR]
       * [[http://bioinfo.cipf.es/noiseq/doku.php?id=tutorial|NOISeq]] [wiki:SOPs/rna-seq-diff-expressions/NOISeq | More detail about NOISeq]