R: A SELDI-TOF data of 167 breast cancer and normal spectra
A SELDI-TOF data of 167 breast cancer and normal spectra
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
As an alternative, package PROcess may be used for
pre-processing of the raw spectra to get a set of proto-biomarkers.
Alex Miron's Lab at the Dana-Farber Cancer Institute.
# plot a raw spectrum
f45c <- system.file("f45c", package="ProData")
fs <- dir(f45c,full.names=TRUE)
# find out sizes of phenotype groups:
SpecGrp <- pData(f45cbmk)
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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,
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> 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)), type="l")
> # find out sizes of phenotype groups:
> SpecGrp <- pData(f45cbmk)
A B C D
55 64 35 13
Created & Maintained by Osamu Ogasawara (firstname.lastname@example.org) and