### R code from vignette source 'vignettes/SLqPCR/inst/doc/SLqPCR.Rnw' ################################################### ### code chunk number 1: SLqPCR ################################################### library(SLqPCR) data(vandesompele) str(vandesompele) ################################################### ### code chunk number 2: fig2 ################################################### tissue <- as.factor(c(rep("BM", 9), rep("POOL", 9), rep("FIB", 20), rep("LEU", 13), rep("NB", 34))) res.BM <- selectHKgenes(vandesompele[tissue == "BM",], method = "Vandesompele", geneSymbol = names(vandesompele), minNrHK = 2, trace = TRUE, na.rm = TRUE) res.POOL <- selectHKgenes(vandesompele[tissue == "POOL",], method = "Vandesompele", geneSymbol = names(vandesompele), minNrHK = 2, trace = FALSE, na.rm = TRUE) res.FIB <- selectHKgenes(vandesompele[tissue == "FIB",], method = "Vandesompele", geneSymbol = names(vandesompele), minNrHK = 2, trace = FALSE, na.rm = TRUE) res.LEU <- selectHKgenes(vandesompele[tissue == "LEU",], method = "Vandesompele", geneSymbol = names(vandesompele), minNrHK = 2, trace = FALSE, na.rm = TRUE) res.NB <- selectHKgenes(vandesompele[tissue == "NB",], method = "Vandesompele", geneSymbol = names(vandesompele), minNrHK = 2, trace = FALSE, na.rm = TRUE) ################################################### ### code chunk number 3: table3 ################################################### ranks <- data.frame(c(1, 1:9), res.BM$ranking, res.POOL$ranking, res.FIB$ranking, res.LEU$ranking, res.NB$ranking) names(ranks) <- c("rank", "BM", "POOL", "FIB", "LEU", "NB") ranks ################################################### ### code chunk number 4: relQuant ################################################### exa1 <- apply(vandesompele[tissue == "BM",], 2, relQuantPCR, E = 2) ################################################### ### code chunk number 5: fig2 ################################################### library(RColorBrewer) mypalette <- brewer.pal(5, "Set1") matplot(cbind(res.BM$meanM, res.POOL$meanM, res.FIB$meanM, res.LEU$meanM, res.NB$meanM), type = "b", ylab = "Average expression stability M", xlab = "Number of remaining control genes", axes = FALSE, pch = 19, col = mypalette, ylim = c(0.2, 1.22), lty = 1, lwd = 2, main = "Gene stability measure") axis(1, at = 1:9, labels = as.character(10:2)) axis(2, at = seq(0.2, 1.2, by = 0.2), labels = as.character(seq(0.2, 1.2, by = 0.2))) box() abline(h = seq(0.2, 1.2, by = 0.2), lty = 2, lwd = 1, col = "grey") legend("topright", legend = c("BM", "POOL", "FIB", "LEU", "NB"), fill = mypalette) ################################################### ### code chunk number 6: fig3a ################################################### mypalette <- brewer.pal(8, "YlGnBu") barplot(cbind(res.BM$variation, res.POOL$variation, res.FIB$variation, res.LEU$variation, res.NB$variation), beside = TRUE, col = mypalette, space = c(0, 2), names.arg = c("BM", "POOL", "FIB", "LEU", "NB")) legend("topright", legend = c("V9/10", "V8/9", "V7/8", "V6/7", "V5/6", "V4/5", "V3/4", "V2/3"), fill = mypalette, ncol = 2) abline(h = seq(0.05, 0.25, by = 0.05), lty = 2, col = "grey") abline(h = 0.15, lty = 1, col = "black") ################################################### ### code chunk number 7: norm ################################################### data(SLqPCRdata) SLqPCRdata (relData <- apply(SLqPCRdata, 2, relQuantPCR, E = 2)) geneStabM(relData[,c(3,4)]) (exprData <- normPCR(SLqPCRdata, c(3,4)))