NEXALEL · MICROBIOME INTELLIGENCE
Informe calculado desde los datos de esta ejecución. Evidencia exploratoria para revisión científica.
DEMO · PUBLIC OR SYNTHETIC DATA · NOT FOR CLINICAL USE
PREGUNTA DE INVESTIGACIÓN
Synthetic counts for software validation; no biological samples.
El paquete conserva las estimaciones, sus condiciones y los archivos que permiten verificarlas. La siguiente decisión es identificar qué hallazgos justifican revisión y replicación.
Contraste ajustado según el plan: -0.066 nats (IC 95% -0.075 a -0.056); p = 3.96e-19. Revisar supuestos del modelo antes de interpretar.
SOURCE · research-statistics.json
METHOD · linear model of Shannon; exploratory, model assumptions require review
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
PERMANOVA Bray–Curtis: R² = 0.186; p = 0.0010. PERMDISP p = 0.0850. La dispersión desigual puede contribuir al resultado; no establece un efecto causal.
SOURCE · research-statistics.json
METHOD · PERMANOVA marginal y PERMDISP; 999 permutaciones
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
2 géneros cumplen q < 0.05 y sensibilidad al manejo de ceros. El criterio prioriza revisión; no valida biomarcadores. Cero señales no demuestra ausencia de efecto.
SOURCE · differential_abundance.tsv · da_status.json
METHOD · ANCOM-BC2, BH dentro del contraste declarado, sensibilidad a pseudoconteos
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
Leemos la cohorte desde tres preguntas: qué cambia al ajustar por contexto, qué muestras son próximas y cuánto depende la geometría de la distancia elegida. El atlas se selecciona por varianza, nunca por significancia.
Estado: computed.
RDA parcial: R² del grupo condicionado = 0.202; R² ajustado = 0.192; p de permutación = 0.002. Dispersión entre grupos: p = 0.082. Bloqueo: unrestricted independent samples.
Un R² ajustado negativo puede indicar que el modelo no mejora el baseline tras penalizar su complejidad. Un p grande no demuestra equivalencia. La dispersión se revisa por separado porque separación de centros y heterogeneidad no son lo mismo.
La red une 60 muestras mediante 59 aristas del árbol mínimo; 100.0% se conservan al cambiar el pseudoconteo. Esa fracción describe sensibilidad de la representación, no confianza en interacciones biológicas. Los nodos de mayor grado no son microorganismos clave.
SOURCE · multivariate-review.json y tablas multivariate-*.tsv
METHOD · Diagnósticos multivariados predefinidos; no selección por resultado
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
Estado: computed. 12 especificaciones; comparación CLR exploratoria de la misma cohorte. No equivale a replicación.
| ID | Prevalencia mínima (fracción) | Pseudoconteo (lecturas) | Ajuste |
|---|---|---|---|
| clr-01 | 0.05 | 0.5 | unadjusted |
| clr-02 | 0.1 | 0.5 | unadjusted |
| clr-03 | 0.2 | 0.5 | unadjusted |
| clr-04 | 0.05 | 1 | unadjusted |
| clr-05 | 0.1 | 1 | unadjusted |
| clr-06 | 0.2 | 1 | unadjusted |
| clr-07 | 0.05 | 0.5 | prespecified |
| clr-08 | 0.1 | 0.5 | prespecified |
| clr-09 | 0.2 | 0.5 | prespecified |
| clr-10 | 0.05 | 1 | prespecified |
| clr-11 | 0.1 | 1 | prespecified |
| clr-12 | 0.2 | 1 | prespecified |
Ocho mayores magnitudes de la especificación de referencia; fracciones calculadas solo sobre ajustes estimables. El TSV conserva todos los taxones y exclusiones.
| Taxón | Estimables/total | Dirección (fracción) | q < 0.05 (fracción) | Rango CLR (log-ratio) |
|---|---|---|---|---|
| SimulatedGenus01 | 12/12 | 1.000 | 1.000 | 1.575 a 1.583 |
| SimulatedGenus02 | 12/12 | 1.000 | 1.000 | -1.480 a -1.467 |
| SimulatedGenus03 | 8/12 | 1.000 | 0.000 | 0.344 a 0.379 |
| SimulatedGenus09 | 12/12 | 1.000 | 0.000 | -0.273 a -0.263 |
| SimulatedGenus06 | 12/12 | 1.000 | 0.000 | -0.202 a -0.195 |
| SimulatedGenus24 | 12/12 | 1.000 | 0.000 | 0.171 a 0.182 |
| SimulatedGenus60 | 12/12 | 1.000 | 0.000 | -0.158 a -0.148 |
| SimulatedGenus42 | 12/12 | 1.000 | 0.000 | -0.138 a -0.131 |
SOURCE · review-dossier.json · specification-curve.tsv
METHOD · Grilla fija CLR; denominadores explícitos
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
SOURCE · multivariate-coordinates.tsv
METHOD · PCA CLR total y residual tras covariables; escalas independientes
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
SOURCE · multivariate-heatmap.tsv
METHOD · 24 géneros de mayor varianza; CLR centrado; clustering promedio
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
SOURCE · multivariate-sample-edges.tsv · multivariate-sample-nodes.tsv
METHOD · Árbol mínimo de similitud entre muestras; no red de interacción microbiana
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
SOURCE · multivariate-procrustes.tsv
METHOD · Procrustes descriptivo CLR / Bray–Curtis; sensibilidad de geometría
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
SOURCE · multivariate-review.json · multivariate-variance.tsv
METHOD · RDA parcial CLR; grupo condicionado a covariables; inercia no causal
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
SOURCE · specification-curve.tsv · review-dossier.json
METHOD · OLS CLR; grilla fija; intervalos t 95%; sensibilidad exploratoria
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
SOURCE · alpha_diversity.tsv
METHOD · Hill q0/q1/q2 observados; sin estandarizar por cobertura
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
SOURCE · composition.tsv.gz
METHOD · Proporciones por muestra; mediana y RIC
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
SOURCE · review-dossier.json
METHOD · PCA CLR a género; pseudoconteo 0.5
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
SOURCE · ordination-loadings.tsv
METHOD · Cargas de los mismos ejes CLR; no causas
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
SOURCE · composition.tsv.gz
METHOD · Proporciones medias, agregación por linaje a género
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
SOURCE · alpha_diversity.tsv
METHOD · Shannon por muestra; caja mediana y RIC, todos los puntos
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
SOURCE · qc.json · alpha_diversity.tsv
METHOD · Profundidad frente a Shannon, sin ajuste causal
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
SOURCE · ordination.json
METHOD · PCoA Bray–Curtis; corrección Lingoes si hay autovalores negativos
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
SOURCE · differential_abundance.tsv
METHOD · ANCOM-BC2; intervalos Wald 95%
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
| Método | Estado | Alcance / motivo |
|---|---|---|
| Validación | Calculado | |
| Composición | Calculado | |
| Diversidad alfa | Calculado | |
| Cambios por participante | Pendiente de requisitos | Diseño transversal con una muestra por participante. |
| Diversidad beta | Calculado | |
| Ordenación | Calculado | |
| Abundancia diferencial | Calculado | |
| Red de asociación | Fuera del alcance de esta ejecución | La inferencia de red no está habilitada para este preset. |
| Predicción | Pendiente de requisitos | La cohorte no sustenta una demostración de generalización; se difiere a un conjunto de datos mayor auditado por separado. |
| Predicción funcional | Pendiente de requisitos | No disponible desde tablas de conteos 16S; no se convierten etiquetas taxonómicas en vías medidas. |
| PERMANOVA | computed | |
| PERMDISP | computed | |
| Modelo de Shannon | computed |
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"limitations": [
"Exploratory, unreviewed research; a group association does not establish diagnosis, treatment benefit or causality.",
"Taxonomic abundance is relative. Collection, extraction, contamination and reference bias may affect results.",
"Richness depends on sequencing depth. Good's coverage is sampling coverage, not a clinical quality certificate.",
"Aitchison geometry depends on the declared pseudocount and aggregation; inspect its sensitivity.",
"Negative and positive assay controls were not evaluated by this count-table analysis.",
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"robust_da_signals": 2
}Lecturas por muestra: mínimo 12,364 · mediana 27,572 · máximo 43,614.
Revisar el diseño y los controles con el equipo científico; fijar el contraste y las covariables antes de una cohorte independiente. Una pérdida de señal al corregir lote, profundidad o selección de participantes cambiaría la interpretación.
| Origen | Datos sintéticos |
|---|---|
| Referencia | Nexalel synthetic fixture; no people or biological conclusions. |
| Conjunto | nexalel-review-challenge.1729 |
| SHA-256 del manifiesto | 4e68c0b66a89fea5b3451f35e689367322859e0f7cf97309613cfa711e4611ac |
| SHA-256 del código y recursos | 54d9b94a8864aa38c5097932f8ec7e9ed0f55dad3c800729c495fad13602b14e |
| Semilla | 1729 |
| Entorno R | R version 4.4.2 (2024-10-31) |
| Revisión científica | Pendiente; el software no asigna aceptación científica |
SOURCE · result-manifest.json y artefactos SHA-256
METHOD · Conteos canónicos → motor R → reporte determinista; sin generación libre de conclusiones
CONFIDENCE · Exploratoria, sin revisión independiente
USE · Investigación
Para reproducir: conservar el bundle, la imagen por digest, el plan y la semilla. El manifiesto enumera los archivos liberados y sus huellas. Imprimir desde el navegador permite exportar este informe a PDF.