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 object “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])

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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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/ProData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ProData
> ### Title: A SELDI-TOF data of 167 breast cancer and normal spectra
> ### Aliases: ProData
> ### Keywords: datasets
> 
> ### ** 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])

 A  B  C  D 
55 64 35 13 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>