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For example, for = 0.05 and m = 10, the Bonferroni-adjusted level is 0.005 and the Šidák-adjusted level is approximately 0.005116. One can also compute confidence intervals matching the test decision using the Šidák correction by computing each confidence interval at the ⋅ {\displaystyle \cdot } (1 − α) 1/ m % level.
RNA-Seq can also be used to determine exon/intron boundaries and verify or amend previously annotated 5' and 3' gene boundaries. Recent advances in RNA-Seq include single cell sequencing, bulk RNA sequencing, [6] 3' mRNA-sequencing, in situ sequencing of fixed tissue, and native RNA molecule sequencing with single-molecule real-time sequencing. [7]
But such an approach is conservative if dependence is actually positive. To give an extreme example, under perfect positive dependence, there is effectively only one test and thus, the FWER is uninflated. Accounting for the dependence structure of the p-values (or of the individual test statistics) produces more powerful procedures. This can be ...
The Bonferroni correction can also be applied as a p-value adjustment: Using that approach, instead of adjusting the alpha level, each p-value is multiplied by the number of tests (with adjusted p-values that exceed 1 then being reduced to 1), and the alpha level is left unchanged.
A hypothesis is rejected at level α if and only if its adjusted p-value is less than α. In the earlier example using equal weights, the adjusted p-values are 0.03, 0.06, 0.06, and 0.02. This is another way to see that using α = 0.05, only hypotheses one and four are rejected by this procedure.
The closed testing principle allows the rejection of any one of these elementary hypotheses, say H i, if all possible intersection hypotheses involving H i can be rejected by using valid local level α tests; the adjusted p-value is the largest among those hypotheses.
The weighted harmonic mean of p-values , …, is defined as = = = /, where , …, are weights that must sum to one, i.e. = =.Equal weights may be chosen, in which case = /.. In general, interpreting the HMP directly as a p-value is anti-conservative, meaning that the false positive rate is higher than expected.
The output of gene expression analysis is typically a table with values representing the expression levels of gene IDs or names in rows and samples in the columns as well as standard errors and p-values. The results in the table can be further visualized using volcano plots and heatmaps, where colors represent the estimated expression level.
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