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← From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline

Research fork · replication · version 1

Between basal lactating and basal pregnant mice, the edgeR quasi-likelihood F-test calls 5245 differentially expressed genes at a false discovery rate of 5%, and the top gene is Csn1s2b with a log2 fold change of 6.08.

572d1745-73b3-4990-81ed-415f67c216e6 · parent snapshot 08d51257fae953ba

Opened by Journal Editor · user id b8dd3c46-c465-4360-b96e-ebb82c1b9574

Source extraction incomplete

This legacy fork has no source-grounded comparison. The journal must extract the published output before execution; a reviewer cannot supply it here.

Where the published number comes from

The published value was extracted from the paper. Reader provenance has not been recorded for this fork.

Location in the source pack
not recorded
Readers
Reader provenance
Not recorded for this fork.
Text read
unknown
Reading version
not recorded

The first control has not been finalised. This fork remains a replication.

Plan, runs and results

  1. 1. Target and materials

    blocked

    The target is registered. A comparison rule and full materials are still needed before a control.

  2. 2. Independent model readings

    blocked

    The journal has recorded no independent readings of this paper for this fork. The corpus's review of the record is partial, and a reading the journal did not take is not a reading it can publish as independent review.

    Two readings of the same source text, and whether they agreed on the decisive fields.

  3. 3. Source resolution

    blocked

    The dataset was resolved and fetched by the executing application, and its checksum is recorded with the run, but the journal has not itself resolved the source or read its licence statement. The executing application reported: no licence statement was read

    resolved by the executing application

  4. 4. Protocol reconstruction

    passed

  5. 5. Control execution

    passed

    The control ran in the Automated Assays application, on that application's own infrastructure, against a public dataset whose checksum is recorded with the run. The journal did not execute it.

  6. 6. Control comparison

    failed

    The run completed and reported no replication outcome against the published result, so there is nothing to compare. The run recorded these outcomes: not_established, not_established, not_established, not_established, not_established, not_established, not_established. A completed analysis is not a successful replication.

  7. 7. Publication

    blocked

    This fork is not published as a successful replication. The run completed and its outcome was not_established; the journal publishes that outcome as the finding, and does not infer a successful control from a completed analysis.