Changes between Version 10 and Version 11 of SOPs/rna-seq-diff-expressions


Ignore:
Timestamp:
08/23/13 10:23:44 (11 years ago)
Author:
gbell
Comment:

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  • SOPs/rna-seq-diff-expressions

    v10 v11  
    9999       * [[http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff|cuffDiff]] (part of the cufflinks package; uses BAM files as input)
    100100       * [[http://www.bioconductor.org/packages/release/bioc/html/DESeq.html|DESeq]] [wiki:SOPs/rna-seq-diff-expressions/DESeq | More detail about DESeq]
    101        * [[http://www.bioconductor.org/packages/release/bioc/html/DEGseq.html|DEGSeq]]
    102101       * [[http://bioinfo.cipf.es/noiseq/doku.php?id=tutorial|NOISeq]] [wiki:SOPs/rna-seq-diff-expressions/NOISeq | More detail about NOISeq]
    103102       * 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]
    … …  
    105104      * [[http://www.bioconductor.org/packages/release/bioc/html/DESeq.html|DESeq]]  [wiki:SOPs/rna-seq-diff-expressions/DESeq | More detail about DESeq]
    106105      * [[http://www.bioconductor.org/packages/release/bioc/html/edgeR.html|edgeR]]  [wiki:SOPs/rna-seq-diff-expressions/EdgeR | More detail about EdgeR]
    107       * [[http://www.bioconductor.org/packages/release/bioc/html/baySeq.html|baySeq]]
    108106      * [[http://bioinfo.cipf.es/noiseq/doku.php?id=tutorial|NOISeq]] [wiki:SOPs/rna-seq-diff-expressions/NOISeq | More detail about NOISeq]
    109107      * 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.