OmicsQuest

Omics projects we rescued

Doublets reported as new cell types, thousands of false-positive genes, spatial bins treated as cells, and screens driven by plate position. Here is how our duo teams found each problem and fixed it.

Single-cell RNA-seq

The novel cell type that was a doublet

A reviewer questioned a 'hybrid' population co-expressing T-cell and macrophage markers. Our re-analysis showed it was doublets and ambient RNA, and uncovered a real, smaller exhausted T-cell state.

Single-cell RNA-seq

4,000 'significant' genes, then 212 real ones

Differential expression between knockout and wild-type microglia reported more than 4,000 significant genes. A reviewer asked why. The answer was pseudoreplication.

Spatial transcriptomics

Visium HD: when 2 µm bins were analyzed as cells

A first-pass analysis clustered raw 2 µm bins and produced dozens of uninterpretable clusters driven by UMI depth. We moved the analysis to segmented cells and 8 µm bins.

In situ spatial transcriptomics

Xenium: the ligand-receptor pair that was segmentation leakage

T cells appeared to express a myeloid ligand and its receptor at once, suggesting autocrine signaling. It was transcript spillover from adjacent cells.

Bulk RNA-seq

Bulk RNA-seq: when batch was perfectly confounded with treatment

A startup's lead program rested on 2,800 differentially expressed genes. The first PCA component was sequencing run, and the run was the treatment.

Image-based profiling

Cell Painting: hits that were well positions

Most 'active' compounds sat in outer wells, and replicate compounds failed to find each other. The phenotypes were mostly position effects.

Live-cell imaging

Live imaging: lineages broken by identity swaps

A lab saw unexpectedly variable cell-cycle times in sister cells. Most of the variability came from tracking errors in crowded fields.

Pipeline engineering

From laptop scripts to a production pipeline

When the only computational scientist left, nobody could reproduce last quarter's results. We rebuilt the analysis as a tested, versioned pipeline the team owns.

Cases are anonymized composites; client details are combined and altered for confidentiality.

Is an analysis not holding up?

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