Hi, I am trying to use the package "globaltest" on samples with 2 treatments and could do with some help..... For input "examplesX" I have arranged my normalised data in a matrix with rows=probe-ids, columns=samples For input "examplesY" I have a vector with the data description (WT or MT) For the genesets I have a list containing probeids for 2 pathways My problem: I don`t seem to be able to read my probeids from a .txt file correctly into a vector called "pathway1" This is how I tried to do it in bioconductor: examplesX<-as.matrix(read.table("normalisedresulttable6reps.txt",heade r=TRUE)) examplesY<-c("WT","MT","WT","MT","WT","MT") pathway1<-as.vector(read.table("Immune-associated-probesetids.txt")) pathway2 <- as.vector(read.table("Inflammatory response-associated-probesetids.txt")) lst <- list(Probes.immune=(pathway1),Probes.Inflammation=(pathway2)) > lst $Probes.immune V1 1 1416292_at 2 1426044_a_at 3 1426207_at 4 1440085_at $Probes.Inflammation V1 1 1425947_at 2 1460251_at 3 1416381_a_at 4 1416657_at //test all genes, this works..but not sure whether I have to specify that there are 2 treatments? gt <- globaltest(examplesX, examplesY,) gt //test only those genes in the genelists in lst, this does not work gt <- globaltest(examplesX, examplesY,lst) gt Error: genesets should be a (list of) vector(s) If I however make my list lst as follows my "pathway1" "pathway2" and "lst" looks different and globaltest works: > pathway1<-c("1416292_at","1426044_a_at","1426207_at","1440085_at","NuG O_emt025263_at","NuGO_emt064290_at","1415697_at","1418133_at") > pathway2<-c("1416292_at","1426044_a_at","1426207_at","1440085_at","NuG O_emt025263_at","NuGO_emt064290_at","1415697_at","1418133_at") > lst <- list(Probes.immune=(pathway1),Probes.Inflammation=(pathway2)) > lst $Probes.immune [1] "1416292_at" "1426044_a_at" "1426207_at" [4] "1440085_at" "NuGO_emt025263_at" "NuGO_emt064290_at" [7] "1415697_at" "1418133_at" $Probes.Inflammation [1] "1416292_at" "1426044_a_at" "1426207_at" [4] "1440085_at" "NuGO_emt025263_at" "NuGO_emt064290_at" [7] "1415697_at" "1418133_at" > gt <- globaltest(examplesX, examplesY,lst) > gt Global Test result: Data: 6 samples with 23865 genes; 2 pathways tested Model: logistic Method: All 10 permutations Genes Tested Statistic Q Expected Q sd of Q Probes.immune 8 8 80.72 35.02 39.695 Probes.Inflammation 8 8 80.72 35.02 39.695 P-value Probes.immune 0.2 Probes.Inflammation 0.2

If the files contain a single column of geneids you can try the following pathway1<-read.table("Immune-associated- probesetids.txt",as.is=TRUE)[[1] ] pathway2<-read.table("Inflammatory response-associated-probesetids.txt",as.is=TRUE)[[1]] Jan Oosting > examplesX<-as.matrix(read.table("normalisedresulttable6reps.tx > t",header=TRUE)) > > examplesY<-c("WT","MT","WT","MT","WT","MT") > pathway1<-as.vector(read.table("Immune-associated-probesetids.txt")) > pathway2 <- as.vector(read.table("Inflammatory > response-associated-probesetids.txt")) > lst <- list(Probes.immune=(pathway1),Probes.Inflammation=(pathway2))