R2 correction archive for JoVE74902
Historical Project and New_Verification entries are retained unchanged. These
records document the old analysis, not necessarily the corrected R2 figure or
interpretation. The authoritative corrected records are in R2_Updates.

Patient pairs explicitly confirmed by authors:
qPCR: NC/DFU, NC1/DFU1, NC2/DFU2, NC3/DFU3, n=4 pairs.
WB: corresponding three rows, n=3 pairs. Technical PCR wells are averaged first.
There is no assumed cross-assay patient mapping beyond within-assay pairing.

Reproduce paired statistics after extracting this ZIP:
Rscript R2_Updates/Analysis_Code/reproduce_paired_assays.R R2_Updates/Source_Data reproduced_stats

Reproduce R2 figures (R 4.5.2; packages listed in source script):
Rscript R2_Updates/Analysis_Code/build_complete_figures.R Project reproduced_figures R2_Updates/work no_old_figure_directory
On non-Windows systems, change only the locale initialization line to a supported
UTF-8 locale. The four scientific figures are generated exclusively with R.
The corrected WGCNA script is also provided for the verified absolute-MM label.

Data limitations: original QC cutoffs, full RunHarmony call and SingleR reference/
annotation settings for the analyzed single-cell object remain unrecovered.
The full Seurat RDS is NOT embedded or publicly deposited. WB background
subtraction/lane quantification records remain incomplete. The instrument project
does not verify all reported qPCR protocol settings. The discovery input was TPM,
not raw counts: discovery-dependent statistics were not revalidated in this R2.
No source values were invented or dropped to force a three-pair qPCR sample size.
