If we plot the distributions, we observe that they cannot have arisen from a log transformation, because there are no values near 0, which would represent unity in a log transformation and is where we would expect most of the data to fall:
df %>%
select(starts_with("Fold")) %>%
gather(key, value) %>%
ggplot(aes(value, color=key)) +
geom_density(n=4096) +
coord_cartesian(xlim=c(-5, 5)) +
guides(color="none")
In fact… are any values -1 < x < 1?
df %>%
select(starts_with("Fold")) %>%
gather(key, value) %>%
filter(value < 1, value > -1) %>%
nrow
## [1] 0
So that’s a no.
Also, the range is somewhat greater than -5, 5:
df %>%
select(starts_with("Fold")) %>%
gather(key, value) %>%
group_by(key) %>%
summarize(min=min(value), max=max(value)) %>%
knitr::kable()
| key | min | max |
|---|---|---|
| Fold-Change(baseline vs. GC) | -12.22470 | 13.65620 |
| Fold-Change(baseline vs. HDL) | -2.90123 | 2.22134 |
| Fold-Change(baseline vs. IFNb) | -8.60802 | 2.58496 |
| Fold-Change(baseline vs. IFNg_TNF) | -43.08150 | 42.17510 |
| Fold-Change(baseline vs. IFNg) | -34.30280 | 10.25130 |
| Fold-Change(baseline vs. IL10) | -4.49985 | 6.08848 |
| Fold-Change(baseline vs. IL13) | -38.88690 | 21.85800 |
| Fold-Change(baseline vs. IL4_upLPS) | -37.23170 | 9.86970 |
| Fold-Change(baseline vs. IL4) | -30.06650 | 16.26230 |
| Fold-Change(baseline vs. LA) | -22.92680 | 11.23740 |
| Fold-Change(baseline vs. LiA) | -29.10950 | 13.60780 |
| Fold-Change(baseline vs. OA) | -42.07400 | 10.46060 |
| Fold-Change(baseline vs. P3C_PGE2) | -113.15200 | 6.67239 |
| Fold-Change(baseline vs. P3C) | -12.13370 | 5.62230 |
| Fold-Change(baseline vs. PA) | -27.37880 | 17.37790 |
| Fold-Change(baseline vs. PGE2) | -42.43130 | 6.28818 |
| Fold-Change(baseline vs. SA) | -32.21920 | 13.58090 |
| Fold-Change(baseline vs. sLPS_IC) | -29.75090 | 18.98120 |
| Fold-Change(baseline vs. sLPS_IFNg) | -72.52780 | 49.97010 |
| Fold-Change(baseline vs. sLPS) | -38.95170 | 20.89660 |
| Fold-Change(baseline vs. TNF_P3C) | -22.70020 | 9.19451 |
| Fold-Change(baseline vs. TNF_PGE2) | -36.85690 | 14.10300 |
| Fold-Change(baseline vs. TNF) | -28.13700 | 25.34570 |
| Fold-Change(baseline vs. TPP_IFNb_IFNg) | -65.32070 | 49.69360 |
| Fold-Change(baseline vs. TPP_IFNb) | -57.88370 | 32.16020 |
| Fold-Change(baseline vs. TPP) | -34.85550 | 15.07780 |
| Fold-Change(baseline vs. upLPS_IC) | -16.73070 | 28.79890 |
| Fold-Change(baseline vs. upLPS) | -8.75729 | 4.55696 |