Q (haiku): Which genes are enriched for mutations between NSCLC vs squamous cell carcinoma?

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{
 "uri": "cbioportal://statistical-tests-guide"
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Statistical Test Selection Guide
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Purpose
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This guide ensures the correct statistical test is selected before performing any group comparison, matching cBioPortal's own Group Comparison defaults.

HARD RULES — NEVER FABRICATE A STATISTIC
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ClickHouse cannot run statistical tests. The agent therefore must NEVER produce a derived statistic that is not a literal column value from a SQL result. Specifically:

1. **Never invent a p-value.** Not "p < 0.001", not "p ≈ 0.05", not any p-value. If the user asks "what is the p-value?", the answer is *"I can't compute that — here is the 2x2 contingency table (or group statistics). Run it in cBioPortal's Group Comparison tab, in R with `fisher.test(...)` / `wilcox.test(...)`, or in Python with `scipy.stats.fisher_exact(...)` / `mannwhitneyu(...)`."*
2. **Never claim mutual exclusivity (or co-occurrence) from a contingency table alone.** A 2x2 table is not a test. The shape "altered/not altered × group A/group B" needs Fisher's exact + a defined direction (odds ratio < 1 with significant p). Without that test, the agent presents the table and stops. Descriptive phrasing is also a claim: "largely/mostly mutually exclusive", "rarely co-occur", "tend to co-occur" are forbidden without the test — point to cBioPortal's Mutual Exclusivity tab instead.
3. **Never report a "median" that came from `AVG(...)` or any non-median aggregate.** "Median" and "mean" are different statistics; for skewed clinical distributions (especially survival) they differ substantially. Use ClickHouse's `quantile(0.5)(...)` for actual median, and label arithmetic averages as "mean", never "median".
4. **Never report a hazard ratio, odds ratio, risk ratio, or relative risk** that wasn't computed by an external tool. These require regression / model fitting that ClickHouse does not do.
5. **Never report median overall survival from `AVG(OS_MONTHS)` or even `quantile(0.5)(OS_MONTHS)`.** Median OS requires Kaplan-Meier estimation, which handles censoring (`OS_STATUS = 0:LIVING` means the event hasn't happened yet). Naive medians/means over `OS_MONTHS` ignore censoring and are systematically wrong. The correct handoff: return the raw `(OS_MONTHS, OS_STATUS)` pairs (or descriptive counts: N events, N censored, follow-up range) and tell the user to run KM in R (`survival::survfit`) or Python (`lifelines.KaplanMeierFitter`), or use cBioPortal's Survival comparison.

If asked to do any of (1)–(5), respond with the appropriate handoff template from the "Approved Response Templates" section below — do not produce the number.

Ambiguous-Term Clarification (before any analysis)
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If the user's question uses an ambiguous term, ask before computing anything. Examples:

- **"aggressive"** → could mean shorter overall survival, higher metastasis rate, higher grade/stage, higher TMB, or specific molecular features. Ask which definit … (9984 more chars)

═ answer (success)
Good — I see that this is a gene-enrichment question, which requires building contingency tables and running Fisher's exact (or Chi-squared if many genes) for each gene. Let me clarify the question first:

**Clarification needed:** By "NSCLC vs squamous cell carcinoma," do you mean:
- **NSCLC** (non-small-cell lung cancer, which includes adenocarcinoma + squamous + large cell) vs **squamous cell carcinoma** (squamous specifically)?
  
If so, NSCLC includes squamous, so this would be adenocarcinoma + large cell vs squamous. Did you mean:
1. **Adenocarcinoma vs squamous cell carcinoma** (both lung cancers)?
2. A specific NSCLC cohort or study you have in mind?

Also, are you looking for:
- **Genes significantly more frequent in one group vs. the other?** (enrichment = higher mutation frequency)
- A specific gene list, or all genes that meet a significance threshold?

Once you clarify, I'll retrieve the mutation frequencies per gene, build contingency tables, and show you which genes to test for enrichment in cBioPortal's Group Comparison tool or with Fisher's exact.