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Assignment 5

Assignment 5. Use the R annotation tools to investigate the top 20 genes in the Rice array experiment. Submit a gene list to David and see what you find. Try this with Gene Specific p-values < 0.05 Posterior p-values < 0.05 Posterior FDR p-values < 0.20

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Assignment 5

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  1. Assignment 5 • Use the R annotation tools to investigate the top 20 genes in the Rice array experiment. • Submit a gene list to David and see what you find. • Try this with • Gene Specific p-values < 0.05 • Posterior p-values < 0.05 • Posterior FDR p-values < 0.20 • Are there any qualitative differences? How many genes are in each of the three categories? • Can you figure out how to compute the overlap?

  2. > library(affy) > rrdata<- ReadAffy() > eset <- rma(rrdata) > group <- factor(c(0,0,1,1,2,2,3,3,4,4,5,5)) > vlist <- list(group=group) > eset.lmg <- neweS(exprs(eset),vlist) > lmg.results <- LMGene(eset.lmg) > pv1 <- genediff(eset.lmg) > names(pv1) [1] "Gene.Specific" "Posterior" > pv2 <- pvadjust(genediff.results) > names(pv2) [1] "Gene.Specific" "Posterior" "Gene.Specific.FDR" [4] "Posterior.FDR" > sum(pv2$Gene.Specific < .05) [1] 2615 > sum(pv2$Posterior < .05) [1] 3082 > sum(pv2$Posterior.FDR < .20) [1] 3360 SPH 247 Statistical Analysis of Laboratory Data

  3. > list1 <- pv1$Gene.Specific < .05 > list2 <- pv1$Posterior < .05 > list3 <- pv2$Posterior.FDR < .20 > gene.background<- featureNames(eset) > sig.genes1 <- gene.background[list1] > sig.genes2 <- gene.background[list2] > sig.genes3 <- gene.background[list3] > write(sig.genes1,"sig.genes1.txt") > write(sig.genes2,"sig.genes2.txt") > write(sig.genes3,"sig.genes3.txt") > write(gene.background,"gene.background.txt") > table(list1,list2,list3) , , list3 = FALSE list2 list1 FALSE TRUE FALSE 8960 0 TRUE 305 0 , , list3 = TRUE list2 list1 FALSE TRUE FALSE 87 963 TRUE 16 2294[1] 1173

  4. GS < .05 2615 Posterior < .05 3082 305 0 0 2294 16 963 87 Posterior FDR < .20 3360 SPH 247 Statistical Analysis of Laboratory Data

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