Residual Disease Paper ======================================================== Plotting RD Status -------------------------------------------------------- by Shelley Herbrich *May 8, 2013* ## 1 Executive Summary ### 1.1 Introduction In this report, we present the script used to display RD by ADH1B and FABP4. ### 1.2 Data & Methods We use the "PCRResults.RData" file which contains the sample-specific source, plate, randomized sample identifier, ADH1B and FABP4 quantifications, RD call, and true RD status. ### 1.3 Results We generate a plot of the ADH1B versus FABP4 PCR values indicating samples with RD by red points. The solid vertical line corresponds to the final threshold used to identify samples with high FABP4 (top 25%). The dashed line shows the partitioning of samples using both FABP4 and ADH1B. ## 2 Loading Data First, we load the deidentified PCR results. ```r load(file.path("RDataObjects", "PCRResults.RData")) ``` ## 3 Plotting PCR Data We plot the PCR measurements for ADH1B against FABP4 indicating RD in red. ```r pdf(file = "plottingRD.pdf", paper = "USr") rd <- factor(PCRResults$RDStatus) plot(PCRResults$FABP4, PCRResults$ADH1B, pch = 21, bg = c("grey", "red")[rd], xlab = "FABP4", ylab = "ADH1B") legend("topleft", c("RD", "no RD"), pch = 19, col = c("red", "grey"), bty = "n", cex = 0.8) abline(v = -20.05) abline(a = -39.5, b = -1, lty = 2) dev.off() ``` ``` ## pdf ## 2 ``` ## 4 Appendix ```r getwd() ``` ``` ## [1] "\\\\mdadqsfs02/workspace/kabagg/RDPaper/Webpage/ResidualDisease" ``` ```r sessionInfo() ``` ``` ## R version 2.15.3 (2013-03-01) ## Platform: x86_64-w64-mingw32/x64 (64-bit) ## ## locale: ## [1] LC_COLLATE=English_United States.1252 ## [2] LC_CTYPE=English_United States.1252 ## [3] LC_MONETARY=English_United States.1252 ## [4] LC_NUMERIC=C ## [5] LC_TIME=English_United States.1252 ## ## attached base packages: ## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: ## [1] knitr_1.2 ## ## loaded via a namespace (and not attached): ## [1] digest_0.6.3 evaluate_0.4.3 formatR_0.7 stringr_0.6.2 ## [5] tools_2.15.3 ```