Residual Disease Paper ======================================================== Comparing Ovary and Omentum Expression ------------------------------------------------------- by Shelley Herbrich *May 13, 2013* ```{r options, echo=FALSE} opts_chunk$set(tidy=TRUE, message=FALSE, warning=FALSE) ``` ## 1 Executive Summary ### 1.1 Introduction In this report, we compare the PCR expression of our target genes between ovary and omental samples. ### 1.2 Data & Methods Here, we use PCR quantification summaries of samples run on the 17 plates containing tissue from both ovary and omentum. ### 1.3 Results We produce density plots of ADH1B and FABP4 expression by tissue. We see that for both genes, omental levels are markedly higher than ovary. ## 2 Loading PCR Data ```{r libraries} library(RColorBrewer) ``` ```{r loadPCRFiles} load(file.path("RDataObjects","OMResults.RData")) load(file.path("RDataObjects","PCRResults.RData")) ``` ```{r matchPlates} #match plates plate <- unique(OMResults$Plate) ovFABP4 <- PCRResults$FABP4[which(PCRResults$Plate %in% plate)] ovADH1B <- PCRResults$ADH1B[which(PCRResults$Plate %in% plate)] ``` ## 3 Plotting Densities of ADH1B and FABP4 Expression ```{r plotDensities} #pdf(file="OVOMExpression.pdf",paper="USr") plot(density(ovADH1B), col="red", xlim=c(-30,-5), main="ADH1B Expression") lines(density(OMResults$ADH1B),col="grey") legend("topright",c("Ovary","Omentum"),col=c("red","grey"),lty=1,bty="n") plot(density(ovFABP4), col="red", xlim=c(-30,-5), main="FABP4 Expression") lines(density(OMResults$FABP4),col="grey") legend("topright",c("Ovary","Omentum"),col=c("red","grey"),lty=1,bty="n") #dev.off() ``` ## Appendix ```{r getLocation} getwd() ``` ```{r sessionInfo} sessionInfo() ```