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Untargeted and targeted lipidomics – statistical analysis: Factoria ANOVA in R

LC Lucas Carminatti Pantaleao
II Isabella Inzani
SO Susan E Ozanne

Last updated date: Jul 15, 2022 Views: 547 Forks: 0

original An abbreviated version of this protocol was published in eLife in Jan, 2022
Maternal diet-induced obesity during pregnancy alters lipid supply to mouse E18.5 fetuses and changes the cardiac tissue lipidome in a sex-dependent manner
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#gp.st is a data frame object containing the lipid classes (columns) abundance for each individual sample (rows)

#mtdt2.cl is a data frame object containing samples' metadata (e.g: sex, maternal group, etc) organized in columns.

 

BiocManager::install("car")

library(car)
anv<-apply(gp.st,2,function(x){a<-cbind("lipid"= x,"sex"=mtdt2.cl$sex,"group"=mtdt2.cl$group)
a<-as.data.frame(a)
a$lipid<-as.numeric(as.character(a$lipid))
model=lm(lipid ~ group + sex + group:sex, data = a)
b<-Anova(model, type="II")
c<-b$`Pr(>F)`[1:3]
})
rownames(anv)<-c("group","sex","group:sex")  

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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Carminatti Pantaleao, L, Inzani, I and Ozanne, S(2022). Untargeted and targeted lipidomics – statistical analysis: Factoria ANOVA in R. Bio-protocol Preprint. bio-protocol.org/prep1799.
  2. Pantaleão, L. C., Inzani, I., Furse, S., Loche, E., Hufnagel, A., Ashmore, T., Blackmore, H. L., Jenkins, B., Carpenter, A. A. M., Wilczynska, A., Bushell, M., Koulman, A., Fernandez-Twinn, D. S. and Ozanne, S. E.(2022). Maternal diet-induced obesity during pregnancy alters lipid supply to mouse E18.5 fetuses and changes the cardiac tissue lipidome in a sex-dependent manner. eLife. DOI: 10.7554/eLife.69078

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