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Table 2 Validation of two pooling strategies for RNA-Seq

From: Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq

Parametersa Pooling 3 samples Pooling 8 samples
Total number of identified DEGsb 4175 2513
Sensitivity (True positivity rate) (%) 93.75 90.24
Specificity (True negativity rate) (%) 81.27 86.59
False positivity rate (%) 18.73 13.41
False negativity rate (%) 6.25 9.76
Positive predictive value (%) 0.36 2.94
Negative predictive value (%) 99.99 99.95
Agreement between identified DEGsc 0.006 0.049
Correlation between reported LFCd 0.380 0.517
Root-mean-square deviation of LFCe 1.198 0.518
  1. aSequencing corresponding individual biological samples was the reference standard
  2. bDifferentially Expressed Genes (DEGs), after Benjamini-Hochberg false discovery correction at an expected rate of 5 %
  3. cInter-rater agreement Cohen’s kappa between sequencing individual samples (3 or 8/group) and sequencing pooled samples (3 or 8 biological replicates/pool; 2 pools/group) to identify DEGs
  4. dSpearman correlation coefficient between the logarithmic fold changes (LFC), which were estimated by sequencing individual samples and by sequencing pooled samples
  5. eStandard deviation of the differences between the LFC, estimated by sequencing individual samples and by sequencing pooled samples