Residual Disease Paper
========================================================
Comparing Ovary and Omentum Expression
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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()
```
