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Table 1 Fold difference in the expression values of informative probe sets for 3 different clinical prediction problems assessed in the same breast cancer data set (GEO GSE 16716)

From: Lack of sufficiently strong informative features limits the potential of gene expression analysis as predictive tool for many clinical classification problems

  ER+ versus ER- 1 pCR versus RD 2 pCR versus RD in ER- cancers only 3
  Feature # 10 Feature # 100 Feature # 10 Feature # 100 Feature # 10 Feature # 100
FDR adjusted p-value 4.71E-12 3.26E-07 0.004 0.0205 0.4 0.68
Fold difference4      
< 0.5 0 0 0 6 4 59
≥0.5 - < 1.0 0 13 3 43 2 32
≥1.0 - < 1.2 0 8 1 15 4 7
≥1.2 - < 1.5 0 18 2 17 0 1
≥1.5 - < 2.0 0 18 2 11 0 1
≥ 2.0 - < 3.0 6 28 2 8 0 0
≥ 3.0 - < 4.0 3 12 0 0 0 0
≥ 4.0 1 3 0 0 0 0
  1. 1 Random sample of 41 ER Positive and 50 ER Negative Samples
  2. 2 Random sample of 41 pathologic CR and 50 residual cancers regardless of ER status.
  3. 3 Random sample of 41 pathologic CR and 50 residual cancers all ER Negative.
  4. 4 Log2 Difference = abs(mean log2 intensity for group1 - mean log2 intensity for group 2) where "abs" is absolute value.
  5. The numbers of probe sets with a given level of differential expression are shown for the 3 comparisons including (i) Estrogen Receptor (ER)-positive versus ER-negative cancers, (ii) cancers with pathologic complete response (pCR) to chemotherapy versus lesser response (RD) and (iii) cases with pCR versus RD in ER-negative cancers only. Probe sets with mean log2 transformed expression difference > 1 between comparisons groups are highlighted in bold. FDR = false discovery rate (i.e., proportion of genes detected to be informative which are not truly informative). FDR adjusted p-values (also known as FDR q-values) are the estimated FDR values that would be incurred if the p-values associated with the selected genes were used as the threshold for significance (i.e., genes with that p-value or a lower p-value were to be detected as informative). So for the Feature #10 column, the reported FDR adjusted p-value is the q-value associated with the 10th highest ranked gene.