\HeaderA{f45cbmk}{A SELDI-TOF data of 167 breast cancer and normal samples from the Miron Laboratory}{f45cbmk}
\keyword{datasets}{f45cbmk}
\begin{Description}\relax
The data consist of 167 SELDI-TOF spectra from either individuals 
with breast cancer or without (normal controls). Two covariates
are available. The data have been pre-processed by Ciphergen's
software and the specific details are as follows.  The baselines 
of the spectra were subtracted using the default parameter 
settings of the Ciphergen software, and the spectra were 
normalized by the total ion current normalization function of 
the Ciphergen software. Peaks were detected with signal to noise 
ratio (S/N) above 10. Proto-biomarkers, i.e., peaks in each 
spectrum that have the same M/Z value, were detected with the 
following parameters: first pass, 10 S/N, min peak threshold 
10
pass, 5 S/N, and add estimated peaks to complete clusters and 
it is the jointly normalized data that are available here. 
The data are presented in the form of an \code{exprSet} object.
\end{Description}
\begin{Usage}
\begin{verbatim}data(f45cbmk)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The different covariates are:
\describe{
\item[GROUP:] a character vector with four possible 
values, "A", "B", "C" and "D".  "A" represents HER2 
positive patients, "B" normal healthy patients, "C" 
ER/PR positive patients and "D" samples from a single 
healthy woman.
\item[SPECTRUM:] a character vector, the spectrum id of 
each sample.
}
\end{Format}
\begin{Source}\relax
Alex Miron's Lab at the Dana-Farber Cancer Institute.
\end{Source}
\begin{References}\relax
Shi, Q. et al. Biomarker Discovery in Plasma Using Proteomics Ana
lysis for Early Detection of Breast Cancer. 2004, manuscript.
\end{References}
\begin{Examples}
\begin{ExampleCode}
data(f45cbmk)
\end{ExampleCode}
\end{Examples}

