Table 1 Analysis choices of various studies of the "Golden Spike" data set. These are choices we believe were made for each of the six stages of the analysis pipeline we have outlined.
Study | Summarization method | Post-summ Normalization | DE method | Dir | True positives | True negatives |
|---|---|---|---|---|---|---|
Choe et al. [4] | CP, MAS5.0, RMA, GCRMA, MBEI plus many variants of these | none, loess_invariant | t-test, Cyber-T, SAM | either | FC >1 | invariant |
Liu et al. [13] | CP, multi-mgMOS | loess_invariant | Cyber-T, PPLR | up | FC >1 | invariant |
Hochreiter et al. [15] | MAS5.0, RMA, MBEI and FARMS | none | SAM | up | FC >1 | invariant |
Chen et al. [16] | CP, MAS5.0, RMA, GCRMA, MBEI, PLIER, FARMS and DFW | none | FC | either | FC >1 and FC = x(for all x) | invariant |
Current study | CP, MAS5.0, RMA, GCRMA, MBEI, multi-mgMOS, FARMS, DFW, PLIER | none, loess_invariant, loess_equal, loess_all | FC, t-test, Cyber-T, limma and PPLR | either, up and down | FC >1, low FC, medium FC, high FC and FC = x(for all x) | equal and invariant |