Comparing GenTox with Bacterial.Mutagenesis

compare_tggates_drugmatrix.Rmd

# Comparing GenTox with Bacterial.Mutagenesis

```{r}
library(Biobase)

setwd(file.path("C:","Users","djenk","OneDrive","grad_school","05-2015_fall",
                "BS830_microarray","20151218-Final_Project"))

#TG-GATEs Data (Discovery Set)
load("Rat.Liver.in_vivo.repeat.annotated.RData")
tg.gates <- eSet

#Drug Matrix (Validation Set)
load("DM_liver_only.RData")
drug.matrix <- data_curated
rm(data_curated,eSet)
```

Here are the drugs that are in drug.matrix and TG-GATEs

```{r}
intersect(unique(pData(drug.matrix)[,c("CHEMICAL")]),unique(as.character(pData(tg.gates)[,c("Chemical")])))
```

Here are three drugs that seem to have different GenTox and Bacterial Mutagenesis columns. Everything else lines up except for four compounds that are listed as "NA" in TG-GATEs GenTox and have a value in Bacterial.Mutagenesis

```{r}
pData(drug.matrix)[,c("CHEMICAL","GenTox")][grepl("carbon tetrachloride",pData(drug.matrix)[,c("CHEMICAL")]),]
pData(tg.gates)[,c("Chemical","Bacterial.Mutagenesis")][grepl("carbon tetrachloride",pData(tg.gates)[,c("Chemical")]),]

pData(drug.matrix)[,c("CHEMICAL","GenTox")][grepl("indomethacin",pData(drug.matrix)[,c("CHEMICAL")]),]
pData(tg.gates)[,c("Chemical","Bacterial.Mutagenesis")][grepl("indomethacin",pData(tg.gates)[,c("Chemical")]),]

pData(drug.matrix)[,c("CHEMICAL","GenTox")][grepl("methapyrilene",pData(drug.matrix)[,c("CHEMICAL")]),]
pData(tg.gates)[,c("Chemical","Bacterial.Mutagenesis")][grepl("methapyrilene",pData(tg.gates)[,c("Chemical")]),]
```