Changes between Version 36 and Version 37 of SOPs/rna-seq-diff-expressions


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Timestamp:
04/27/17 08:31:14 (8 years ago)
Author:
gbell
Comment:

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  • SOPs/rna-seq-diff-expressions

    v36 v37  
    105105    * Some statistical tests or packages can be applied to non-replicated data (but must be interpreted with a high degree of caution):
    106106       * [[http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff|cuffDiff]] (part of the cufflinks package; uses BAM files as input)
    107        * [[http://www.bioconductor.org/packages/release/bioc/html/DESeq.html|DESeq]] [wiki:SOPs/rna-seq-diff-expressions/DESeq | More detail about DESeq]
    108        * [[http://bioinfo.cipf.es/noiseq/doku.php?id=tutorial|NOISeq]] [wiki:SOPs/rna-seq-diff-expressions/NOISeq | More detail about NOISeq]
    109        * 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]
     107       * [[http://www.bioconductor.org/packages/release/bioc/html/DESeq.html|DESeq]] ([wiki:SOPs/rna-seq-diff-expressions/DESeq more detail])
     108       * [http://www.bioconductor.org/packages/release/bioc/html/NOISeq.html NOISeq] ([wiki:SOPs/rna-seq-diff-expressions/NOISeq more detail])
     109       * 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])
    110110    * Some statistical tests or packages are designed for experiments with replication:
    111       * [[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.)
     111      * [[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.)
    112112      * [[http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html|DESeq2]]  (We haven't compared this with DESeq very thoroughly.)
    113       * [[http://www.bioconductor.org/packages/release/bioc/html/edgeR.html|edgeR]]  [wiki:SOPs/rna-seq-diff-expressions/EdgeR | More detail about EdgeR]
    114       * [[http://bioinfo.cipf.es/noiseq/doku.php?id=tutorial|NOISeq]] [wiki:SOPs/rna-seq-diff-expressions/NOISeq | More detail about NOISeq]
     113      * [[http://www.bioconductor.org/packages/release/bioc/html/edgeR.html|edgeR]]  ([wiki:SOPs/rna-seq-diff-expressions/EdgeR more detail])
     114      * [http://www.bioconductor.org/packages/release/bioc/html/NOISeq.html NOISeq] ([wiki:SOPs/rna-seq-diff-expressions/NOISeq more detail])
    115115      * 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.
    116116    * 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).
    … …  
    171171      * [[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.
    172172      * [[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.
    173    * For more practical information, see the third session of [http://jura.wi.mit.edu/bio/education/R2011/ | An introduction to R and Bioconductor: A BaRC Short Course] and the BaRC Hot Topic [http://jura.wi.mit.edu/bio/education/hot_topics/RNAseq/RNAseqDE_Dec2011.pdf | RNA-seq: A practical guide to the analysis of differential gene expression ]
     173   * For more practical information, see the third session of [http://jura.wi.mit.edu/bio/education/R2011/ An introduction to R and Bioconductor: A BaRC Short Course] and the  [http://jura.wi.mit.edu/bio/hot_topics/ BaRC Hot Topic] (under "Short Read Sequencing", see "Practical RNA-Seq analysis")