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Table 1 GRSN reduces standard deviation while preserving introduced fold change in a simulated data study.

From: Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data

Stage of data simulation

Avg. SD of replicates

Avg. abs FC, samples B vs. A

 

All Genes

Up & Dn Genes

Up Genes

Dn Genes

Sim. FC

15.24

24.37

2.67

-1.92

Sim. Skew

35.49

52.55

2.72

-1.90

GRSN correction

14.68

24.97

2.66

-1.92

  1. Average Standard Deviation (SD) among replicates and average Fold Change (FC) are reported for each stage of our simulated data study (see text for description). SD values for each gene are calculated separately for sample set A and sample set B and then averaged across both sample sets and all 100 simulations. FC values are calculated for each gene by taking the average for sample set B and dividing by the average for sample set A then averaging over all 100 simulations. The values reported in each column are (from left to right) 1) the average SD for all genes, 2) the average SD for the up and down regulated genes, 3) the average FC for up regulated genes, and 4) the average FC for down regulated genes. Values reported in the top row are for data with simulated FC only. Values in the middle row are for data with simulated skew added. The bottom row reports values after GRSN correction of the simulated skew.
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BMC Bioinformatics

ISSN: 1471-2105

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