ProData {ProData} | R Documentation

## A SELDI-TOF data of 167 breast cancer and normal spectra

### Description

This library contains both the raw spectra and the proto-biomarker data pre-processed by Ciphergen's software of the 167 samples. Those one hundred and sixty seven samples are collected from 155 subjects in CPT tubes with plasma isolated and stored in -80C until needed. Among the 167 samples, 55 are HER2 positive (A), 64 are normal healthy women (B), 35 are ER/PR positive (mostly) (C) and 13 samples are from a single healthy woman. Samples in group D are the only ones from a single subject, all the other samples represent draws from individual subjects. Samples were thawed and aliquoted into 100ul vials. The samples were fractionated to simplify the proteome into sub-proteomes. The fractions 4 and 5 (f45) were processed by the Ciphergen IMAC protocol with EAM of CHCA.

Information on the spectrum ID and the pheotype information is stored in the `exprSet` {tt f45cbmk}, the proto-biomakers pre-processed by Ciphergen's software.

As an alternative, package `PROcess` may be used for pre-processing of the raw spectra to get a set of proto-biomarkers.

### Source

Alex Miron's Lab at the Dana-Farber Cancer Institute.

### Examples

    # plot a raw spectrum
    f45c <- system.file("f45c", package="ProData")
    fs <- dir(f45c,full.names=TRUE)
    plot(read.csv(gzfile(fs[1])), type="l")

    # find out sizes of phenotype groups:
    library(Biobase)
    data(f45cbmk)
    SpecGrp <- pData(f45cbmk)
    table(SpecGrp[,1])

[Package ProData version 0.2 Index]