For this vignette we will examine the ALL dataset.  First we load our ReportingTools  package and the data.  This dataset is from a clinical trial in acute lymphoblastic leukemia (ALL) and  is available from Bioconductor.  

```{r message=FALSE, output="hide"}
library(ReportingTools)
library(ALL)
library(hgu95av2.db)
library(genefilter)
library(GOstats)
library(limma)
library(GSEAlm)
library(GSEABase)
data(ALL)

ALL <- ALL[, ALL$mol.biol %in% c('NEG','BCR/ABL') &
    !is.na(ALL$sex)]
ALL$mol.biol <- factor(ALL$mol.biol, 
    levels = c('NEG', 'BCR/ABL'))
ALL <- featureFilter(ALL)
```
First we have an eBayes fit:

```{r results="asis"}
model <- model.matrix(~mol.biol+sex, ALL)
fit <- eBayes(lmFit(ALL, model))
myrep = HTMLReport(reportDirectory = "./",shortName="bigtest", handlers = ReportingTools:::knitrHandlers)

publish(fit, myrep, eSet=ALL, factor=ALL$mol.biol, coef=2, n=100)
```