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Figure 1b shows the statistical significance (by Student's t tests) of differential transcript cluster expression in a volcano plot format along with respective fold changes (FC).
Indeed, as Shaw, Gupta, et al., (2005) and others have pointed out, tests of differential or competing theories are needed in the literature, as are attempts to integrate these alternative theories (see Nyberg and Ployhart, 2013; Shaw et al., 2013).
These p-values from tests of differential expression summarize the statistical significance of the applied test statistic, based on the variation in gene expression and the error variance.
While current best practices emphasize sufficiently powered univariate tests of differential expression, little is known about the factors that affect the statistical power of complex multivariate analysis protocols for high-dimensional molecular signature development.
Because sex-biased dispersal can also contribute to asymmetric gene flow [14] and is sometimes extreme in bats [42], we tested Erophylla for evidence of sex-biased dispersal (sex data were insufficient to test M. waterhousii) through seven independent tests of differential genetic divergence between the sexes [43].
We propose using Fisher's combined p method [ 16] to combine probe level tests of differential expression.
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As a primary end point, we compared each of these models for the ability to identify genes that were differentially expressed, with the NanoString data considered to be the 'true' test of differential expression.
This ratio of species to introduction events (0.13) is similar to that used in a previous test of differential success due to relative brain size among mammals (0.15: [18]).
Figure 2b shows the statistical significance (by Student's t-tests) of differential transcript cluster expression by volcano plots along with respective fold changes (FC) (Fig. 2b), where a transcript cluster constitutes a group of exon clusters (each exon cluster composed of different probes) corresponding to a known or putative gene.
They are compatible with the exact test of differential expression.
Here we use the Student's t-test applied to expression indices as a test of differential gene expression.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com