Changes between Version 5 and Version 6 of SOPs/diff_microarry


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Timestamp:
08/20/14 13:51:40 (10 years ago)
Author:
thiruvil
Comment:

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  • SOPs/diff_microarry

    v5 v6  
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    65 To find differentially expressed genes, sort the data by both log2 ratio and adjusted p-value.  Choose a log2 ratio and p-value cutoff (eg. abs(log2 ratio) > 1 and adjusted p-value of < 0.05), a combination of both p-values and FC should be used to select DE genes [[ https://stat.ethz.ch/pipermail/bioconductor/2007-October/019479.html | [BioC] topTable threshold on p-value and logFC, Reply from Gordon Smyth]].  Another way to examine DE genes is to look at the volcano-plot, the //tips// of "V" in the volcano would generally have these DE genes.  [[br]]
     65To find differentially expressed genes, sort the data by both log2 ratio and adjusted p-value.  Choose a log2 ratio and p-value cutoff (eg. abs(log2 ratio) > 1 and adjusted p-value of < 0.05), a combination of both p-values and FC should be used to select DE genes [[https://stat.ethz.ch/pipermail/bioconductor/2007-October/019479.html | [BioC] topTable threshold on p-value and logFC, Reply from Gordon Smyth]].  Another way to examine DE genes is to look at the volcano-plot, the //tips// of "V" in the volcano would generally have these DE genes.  [[br]]
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