Can I calculate p-value with mean and se values in facet

How can I calculate p-value from sample mean and se? Thanks for your help.

Below is the code that I am using.

ggplot(combine_mean_se2, aes(x=Treatment, y=mean, colour=Treatment))  
  geom_point(size=6) 
  geom_linerange(aes(ymin= mean-se, ymax=mean se), colour="grey10", linewidth=1)  
  #scale_color_manual(values=c("firebrick4", "dodgerblue4"))  
  ylab("Feature Mean and SE")   
  xlab("")  
  facet_wrap(~traits, scales = "free")   
  elitetheme2   
  theme(legend.position = "top",
        strip.text.x = element_text(size = 21, face = "bold"))

here is my data

https://docs.google.com/spreadsheets/d/1q1guxAKosKztNXWO3ey1ZKZm4VU49ub58_C_bZ8TO1k/edit#gid=0

CodePudding user response：

You already calculated the mean and se. It would be best if you had each sample value for statistical testing. The ggpubr package has excellent functions to add p-value and SE in your graphs.

http://www.sthda.com/english/wiki/one-way-anova-test-in-r

CodePudding user response：

I may not be correct on this p value, but please let me know if it isn't and let me know any formula to derive the p value

I used the below formula

z = Est/SE P = exp(−0.717×z − 0.416×z^2)

code

library(rvest)
library(tidyverse)

df <- rvest::read_html('https://docs.google.com/spreadsheets/d/1q1guxAKosKztNXWO3ey1ZKZm4VU49ub58_C_bZ8TO1k/edit#gid=0') %>% html_table()
df2 <- df[[1]][2:17,2:6]
nam <- df[[1]][1,2:6]
nam2 <- (nam %>% pivot_longer(c('A','B','C','D','E')))$value

names(df2) <- nam2
df3 <- df2 %>% mutate(mean=as.numeric(mean), se=as.numeric(se), z=mean/se, 
p=exp(-0.717*z-0.416*z^2))

output

# A tibble: 16 × 7
   Treatment Si    traits   mean    se     z         p
   <chr>     <chr> <chr>   <dbl> <dbl> <dbl>     <dbl>
 1 K-C       0mM   TRL    12246.  861. 14.2  1.08e- 41
 2 K-CSi     4mM   TRL    16164.  979. 16.5  4.38e- 55
 3 K-DS      0mM   TRL     7852.  525. 14.9  9.67e- 46
 4 K-DSSi    4mM   TRL    12417. 1039. 12.0  2.94e- 30
 5 R-C       0mM   TRL    15893.  638. 24.9  1.59e-120
 6 R-CSi     4mM   TRL    23529. 1001. 23.5  6.29e-108
 7 R-DS      0mM   TRL    10988.  312. 35.2  5.44e-236
 8 R-DSSi    4mM   TRL    14063.  818. 17.2  1.70e- 59
 9 K-C       0mM   PRL     6620.  903.  7.33 9.91e- 13
10 K-CSi     4mM   PRL     9237.  662. 14.0  2.96e- 40
11 K-DS      0mM   PRL     3779.  408.  9.26 4.16e- 19
12 K-DSSi    4mM   PRL     6752.  657. 10.3  5.32e- 23
13 R-C       0mM   PRL     9882.  366. 27.0  3.64e-141
14 R-CSi     4mM   PRL    13409. 1138. 11.8  1.87e- 29
15 R-DS      0mM   PRL     5605.  275. 20.4  2.72e- 82
16 R-DSSi    4mM   PRL     8652.  618. 14.0  1.58e- 40