Changes between Version 15 and Version 16 of SOPs/rna-seq-diff-expressions


Ignore:
Timestamp:
01/15/14 14:29:19 (11 years ago)
Author:
gbell
Comment:

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  • SOPs/rna-seq-diff-expressions

    v15 v16  
    9696    * Some statistical tests or packages can be applied to non-replicated data (but must be interpreted with a high degree of caution):
    9797       * [[http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff|cuffDiff]] (part of the cufflinks package; uses BAM files as input)
    98        * [[http://www.bioconductor.org/packages/release/bioc/html/DESeq.html|DESeq]] [wiki:SOPs/rna-seq-diff-expressions/DESeq | More detail about DESeq]
     98       * [[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.)
    9999       * [[http://bioinfo.cipf.es/noiseq/doku.php?id=tutorial|NOISeq]] [wiki:SOPs/rna-seq-diff-expressions/NOISeq | More detail about NOISeq]
    100100       * 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]
    … …  
    104104      * [[http://bioinfo.cipf.es/noiseq/doku.php?id=tutorial|NOISeq]] [wiki:SOPs/rna-seq-diff-expressions/NOISeq | More detail about NOISeq]
    105105      * 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.
    106     * 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)
     106    * 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).
    107107
    108108  * **Identifying differentially expressed genes**
    … …  
    114114 * **Other**
    115115   * Review articles:
     116      * [[http://www.ncbi.nlm.nih.gov/pubmed/24020486|Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data.]] - Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND, Betel D.  Genome Biol. 2013 Sep 10;14(9):R95.
    116117      * [[http://www.ncbi.nlm.nih.gov/pubmed/21106489|A survey of statistical software for analyzing RNA-seq data]] - Gao D, Kim J, Kim H, Phang TL, Selby H, Tan AC, Tong T.  Hum Genomics. 2010 Oct;5(1):56-60.
    117118      * [[http://www.ncbi.nlm.nih.gov/pubmed/21176179|From RNA-seq reads to differential expression results]] - Oshlack A, Robinson MD, Young MD.  Genome Biol. 2010;11(12):220. Epub 2010 Dec 22.