**Figure 2. Digital gene expression analysis.**
Results from the [analysis scripts][1] used to analyze all data from this protocol, illustrated in Figure 2, are displayed in three tables.
- **Table 1. Confirmatory statistical tests.**: Contains the results of the confirmatory statistical analysis using the Wilcoxon signed-rank test, which treats the data as unpaired. Access the analysis script for the statistical tests related to this table [here][2].
- Note: Since these tests may have a longer than average run time, you will notice that the code for each wilcoxon signed-rank test is greyed-out with only the results remaining. A version of the analysis script exists [here][3] with all test code intact.
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- **Table 2. Exploratory statistical tests.**: Contains the results of the exploratory statistical analysis using the Wilcoxon rank-sum test, which treats the data as paired. Access the analysis script for the statistical tests related to this table [here][4].
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- **Table 3. Exploratory statistical tests.**: Contains the results of the additional exploratory analysis which used Wilcoxon rank-sum tests to compare the difference in expression of active genes during c-Myc induction to the difference in expression of silent genes over that same period (e.g. from 0 hr to 24 hr) for the original study (Lin et al., 2012) and this replication attempt (RP:CB). Access the exploratory analysis script [here][5]
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All of the scripts above will call the [data][6] directly from the OSF.
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Additionally, this component contains a folder with all scripts used in the [re-analysis][7] of the [Original Study data][8], the [R script][9] used to sort and filter Replication Study gene expression data, and the [R script][10] used to compare genes in common between the Original and Replication Studies.
[1]: https://osf.io/5gbsw/files/
[2]: https://osf.io/2yj6v/
[3]: https://osf.io/qujas/
[4]: https://osf.io/3k9sb/
[5]: https://osf.io/3k9sb/
[6]: https://osf.io/7fyhk/files/
[7]: https://osf.io/5gbsw/files/
[8]: https://osf.io/nqfxz/
[9]: https://osf.io/d9tn2/
[10]: https://osf.io/nvjkd/
