Changes between Version 53 and Version 54 of SOPs/rna-seq-diff-expressions

Timestamp:

11/14/17 10:26:38 (7 years ago)

Author:

gbell

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -159 +159 @@
        * 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]) (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])
-      * [http://www.bioconductor.org/packages/release/bioc/html/NOISeq.html NOISeq] ([wiki:SOPs/rna-seq-diff-expressions/NOISeq more detail])
+       * [[http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html|DESeq2]]  (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]) 
+       * [[http://www.bioconductor.org/packages/release/bioc/html/edgeR.html|edgeR]]  ([wiki:SOPs/rna-seq-diff-expressions/EdgeR more detail])
+       * [http://www.bioconductor.org/packages/release/bioc/html/NOISeq.html NOISeq] ([wiki:SOPs/rna-seq-diff-expressions/NOISeq more detail])
       * In our hands, all of these methods appear to work fine.  Note, however, that the scale of the p-values from baySeq are much different from those of DESeq and edgeR.  For example, a gene may have a baySeq p-value of 1e-15 but a DESeq p-value of 1e-300.
     * Scripts with sample code are in the BaRC code repository at \\wi-files1\BaRC_Public\BaRC_code\R (and see the vignettes in the R packages linked above).