
# MA plot

The following is a MA plot of the resistant-responsive contrast.

```{r 'maplot'}
library('DiffBind')
dba.plotMA(tamoxifen)
```

# PCA plot

## All

The following graphic is a PCA plot using the affinity data for all sites.

```{r 'pca'}
dba.plotPCA(tamoxifen, DBA_TISSUE, label = DBA_CONDITION)
```

## Only DB

The following graphic is a PCA plot only using the differentially bound sites.

```{r 'pca-db'}
dba.plotPCA(tamoxifen, contrast = 1, th = .05, label = DBA_TISSUE)
```


The MA and PCA plots are further described in the [DiffBind vignette](http://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf).
