# RNA-seq report audit: free sample

Case 0.1.0; computed 2026-08-30. No purchase or account required.

## Your task

A fictional handoff says: “TSPAN6 increases after treatment because its log2 fold change is positive.” Its table actually reports untreated relative to treated.

1. Repair the caption. Identify the numerator and denominator before interpreting a sign.
2. Predict what happens to the effect, standard error and two-sided p value when the comparison is reversed.
3. Decide what you can say about DPM1 at an adjusted-p-value threshold of 0.05. Does not passing that threshold prove no change?

These are the correctly oriented, **treated relative to untreated** reference values:

| Gene | log2 fold change | BH adjusted p value |
| --- | ---: | ---: |
| TSPAN6 | -0.385237 | 9.60e-4 |
| DPM1 | 0.202855 | 0.184 |
| FKBP5 | 4.042655 | 7.44e-26 |

Write your review sentence before trying the online feedback at https://omicswithjohnson.net/cases/rna-seq-report-audit . This is self-study practice, not a certification test.

## Check your reasoning

TSPAN6 is estimated lower after treatment in this model. Reversing this fixed, unshrunken contrast negates the effect and signed Wald statistic; standard error and two-sided p/adjusted-p values remain unchanged. DPM1 has a positive estimate but does not pass 0.05. That does not establish equivalence or no change. None of these results establishes a clinical benefit.

## Method and provenance

airway 1.32.0; GSE52778; Himes et al. 2014. Eight libraries from four paired cell lines. The complete public count assay had 63677 genes; 16139 met the prespecified rule of ten or more counts in four or more libraries. DESeq2 1.52.0, design ~ cell + dex, parametric dispersion, unshrunken effects and two-sided Wald tests; BH with independent filtering at alpha 0.05. Adjustment was not computed on only these three teaching examples. Display-normalized counts retain cell-line differences. The original read-level analysis was not repeated.

Data package and reuse terms (LGPL as declared upstream): https://bioconductor.org/packages/airway/
Original study: https://pubmed.ncbi.nlm.nih.gov/24926665/
Method reference: https://bioconductor.org/packages/3.23/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
The faulty caption and questions are original teaching material, not alleged errors by the source researchers.

The complete case is under review, not available for purchase. This free sample does not include the full exercise pack, answer guide, or personal support.