Skip to main content

Table 1 Number of genes called significant at 10% false discovery rate on isogenic biologic replicates

From: Towards the uniform distribution of null P values on Affymetrix microarrays

Statistic Embryoid blast Myeloid
  4 hours 24 hours 4 hours 24 hours
Standard t (scheme 1) 32 8,038 7,154 331
Cyber t (scheme 2) 1,288 9,769 10,349 4,464
Scheme 4 90 87 268 38
SAM 4,954 14,239 16,644 9,392
  1. Each entry in this table is the number of significant genes when comparing treatment (DMSO + drug) with control (just DMSO) for a cell type (embryoid blast or myeloid) and a time point (4 or 24 hours). All data were subject to quantile-quantile normalization and summarized using RMA. The Benjamini and Hochberg algorithm was used on P values generated by the standard t test, cyber t, and scheme 4 to calculate false discovery rate. The values for SAM were generated by the TIGR Multiple Array Viewer (see Materials and methods) with 100 permutations and the default parameters. DMSO, dimethyl sulfoxide; RMA, Robust Multichip Average; SAM, significance analysis of microarrays.