1

I am a newbie in R programming and seek help in analyzing the Metabolomics data - 118 metabolites with 4 conditions (3 replicates per condition). I would like to know, for each metabolite, which condition(s) is significantly different from which. Here is part of my data

> head(mydata)
  Conditions   HMDB03331   HMDB00699   HMDB00606    HMDB00707    HMDB00725    HMDB00017  HMDB01173
1 DMSO_BASAL 0.001289121 0.001578235 0.001612297 0.0007772231 3.475837e-06 0.0001221674 0.02691318
2 DMSO_BASAL 0.001158363 0.001413287 0.001541713 0.0007278363 3.345166e-04 0.0001037669 0.03471329
3 DMSO_BASAL 0.001043537 0.002380287 0.001240891 0.0008595932 4.007387e-04 0.0002033625 0.07426482
4   DMSO_G30 0.001195253 0.002338346 0.002133992 0.0007924157 4.189224e-06 0.0002131131 0.05000778
5   DMSO_G30 0.001511538 0.002264779 0.002535853 0.0011580857 3.639661e-06 0.0001700157 0.02657079
6   DMSO_G30 0.001554804 0.001262859 0.002047611 0.0008419137 6.350990e-04 0.0000851638 0.04752020

This is what I have so far.

I learned the first line from this post

kwtest_pvl = apply(mydata[,-1], 2, function(x) kruskal.test(x,as.factor(mydata$Conditions))$p.value)

and this is where I loop through the metabolite that past KW test

tCol = colnames(mydata[,-1])[kwtest_pvl <= 0.05]

for (k in tCol){
  output = posthoc.kruskal.dunn.test(mydata[,k],as.factor(mydata$Conditions),p.adjust.method = "BH")
}

I am not sure how to manage my output such that it is easier to manage for all the metabolites that passed KW test. Perhaps saving the output from each iteration appending to excel? I also tried dunn.test package since it has an option of table or list output. However, it still leaves me at the same point. Kinda stuck here.

Moreover, should I also perform some kind of adjusted p-value, i.e FWER, FDR, BH right after KW test - before performing the posthoc test?

Any suggestion(s) would be greatly appreciated.

Pearl_Lo
  • 11
  • 3
  • What's the problem exactly? How you format and save output depends on the context and what you need to do with it. – camille Apr 24 '19 at 21:23
  • Sorry I probably wasn't clear with my question(s). First, I would like to know whether an adjustment on p-values are needed right after KW test (before performing Dunn test), 2nd, I would like to know which condition(s) are significantly different from the other(s) for each metabolites, and their associated p-values. Is there a way that I can put the output into some kind of list/dataframe so I can further keep the ones with pvalue < 0.05 and make a final list with associated metabolites and conditions – Pearl_Lo Apr 24 '19 at 21:33

0 Answers0