### Transcriptome modulation during host shift is driven by secondary metabolites in desert Drosophila ### De Panis et al. ### Molecular Ecology, 2016 ### Differential Expression analysis with NOISeq source("http://bioconductor.org/biocLite.R") biocLite("NOISeq") library(NOISeq) ### Data: D. buzzatii release1 - FPKM normalized-counts with RSEM = 13657 genes mycounts <- read.table("counts_rsem.fpkm", header=TRUE, row.names = 1) head(mycounts) dim(mycounts) myfactors = data.frame( cact.add_alk = c("op_n", "op_y", "tr_n", "tr_y", "op_n", "op_y", "tr_n", "tr_y", "op_n", "op_y", "tr_n", "tr_y"), add_alk = c("n", "y", "n", "y", "n", "y", "n", "y", "n", "y", "n", "y") ) #treatment=cact.add_alk #op_n: Native O. sulphurea #op_y: O. sulphurea + alkaloids #tr_n: Native T. terscheckii #tr_y: T. terscheckii + alkaloids #added alkaloids condition=add_alk #n: no #y: yes mydata = readData(data = mycounts, factors = myfactors) class(mydata) # Op.Nat_vs_Tr.Nat = noiseqbio(mydata, k = NULL, norm = "n", factor = "cact.add_alk", conditions = c("op_n", "tr_n"), filter = 1) Op.Alk_vs_Tr.Alk = noiseqbio(mydata, k = NULL, norm = "n", factor = "cact.add_alk", conditions = c("op_y", "tr_y"), filter = 1) # # Op.Nat_vs_Op.Alk = noiseqbio(mydata, k = NULL, norm = "n", factor = "cact.add_alk", conditions = c("op_n", "op_y"), filter = 1) Tr.Nat_vs_Tr.Alk = noiseqbio(mydata, k = NULL, norm = "n", factor = "cact.add_alk", conditions = c("tr_n", "tr_y"), filter = 1) # # Op.Nat.AND.Tr.Nat_vs_Op.Alk.AND.Tr.Alk = noiseqbio(mydata, k = NULL, norm = "n", factor = "add.alk", conditions = c("n", "y"), filter = 1) # #RESULTS # head(degenes(Op.Nat_vs_Tr.Nat, q = 0.95, M = NULL)) # 3617 DEGs head(degenes(Op.Nat_vs_Tr.Nat, q = 0.99, M = NULL)) # 41 DEGs head(degenes(Op.Alk_vs_Tr.Alk, q = 0.95, M = NULL)) # 22 DEGs head(degenes(Op.Alk_vs_Tr.Alk, q = 0.99, M = NULL)) # 19 DEGs # # head(degenes(Op.Nat_vs_Op.Alk, q = 0.95, M = NULL)) # 1039 DEGs head(degenes(Op.Nat_vs_Op.Alk, q = 0.99, M = NULL)) # 58 DEGs head(degenes(Tr.Nat_vs_Tr.Alk, q = 0.95, M = NULL)) # 36 DEGs head(degenes(Tr.Nat_vs_Tr.Alk, q = 0.99, M = NULL)) # 20 DEGs # # head(degenes(Op.Nat.AND.Tr.Nat_vs_Op.Alk.AND.Tr.Alk, q = 0.95, M = NULL)) # 34 DEGs head(degenes(Op.Nat.AND.Tr.Nat_vs_Op.Alk.AND.Tr.Alk, q = 0.99, M = NULL)) # 5 DEGs #