In the provided example, isn’t the fact that the results change with respect to the software…
Marc Legault
1

In the provided example, the differences are custom chip description files. These are annotation files expected to change over time as we learn more about the genome. The fact that the results change with different annotation files is not a bug, just a reflection of the knowledge at the time the chip description file was created.

We don’t aim to ensure “correctness” but offer a platform for computational replication so that readers can achieve the same results and draw their own conclusions.

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