A SELDI-TOF data of 167 breast cancer and normal samples from the Miron Laboratory

Description

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 exprSet object.

Usage

data(f45cbmk)

Format

The different covariates are:

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.

SPECTRUM

a character vector, the spectrum id of each sample.

Source

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

References

Shi, Q. et al. Biomarker Discovery in Plasma Using Proteomics Analysis for Early Detection of Breast Cancer. 2004, manuscript.

Examples

data(f45cbmk)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(ProData)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ProData/f45cbmk.Rd_%03d_medium.png", width=480, height=480)
> ### Name: f45cbmk
> ### Title: A SELDI-TOF data of 167 breast cancer and normal samples from
> ###   the Miron Laboratory
> ### Aliases: f45cbmk
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(f45cbmk)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>