Supported by Dr. Osamu Ogasawara and  providing  . |
|
Last data update: 2014.03.03 |
Data from the hyperLOPIT technology on Mouse E14TG2a embryonic stem cellsDescriptionThis is a spatial proteomics dataset from a hyperLOPIT experimental design on Mouse E14TG2a embryonic stem cells Usagedata(hyperLOPIT2015) data(hyperLOPIT2015ms3r1) data(hyperLOPIT2015ms3r2) data(hyperLOPIT2015ms3r3) data(hyperLOPIT2015ms2) FormatThe data is an instance of class DetailsThis is a hyperLOPIT experiment. Normalised intensities for proteins
for TMT 10-plex labelled fractions are available for 3 replicates
acquired in MS3 mode ( SourceThe data was generated by A. Christoforou and C. Mulvey in the Cambridge Centre for Proteomics. http://www.bio.cam.ac.uk/proteomics/. ReferencesChristoforou A, Mulvey CM, Breckels LM, Hayward PC, Geladaki E, Hurrell T, Naake T, Gatto L, Viner R, Martinez Arias A, Lilley KS. A draft map of the mouse pluripotent stem cell spatial proteome Nature Communications, Accepted, October 2015 Examplesdata(hyperLOPIT2015) hyperLOPIT2015 pData(hyperLOPIT2015) head(exprs(hyperLOPIT2015)) 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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(pRolocdata)
Loading required package: MSnbase
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
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics
This is MSnbase version 1.20.7
Read '?MSnbase' and references therein for information
about the package and how to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
This is pRolocdata version 1.10.0.
Use 'pRolocdata()' to list available data sets.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pRolocdata/hyperLOPIT2015.Rd_%03d_medium.png", width=480, height=480)
> ### Name: hyperLOPIT2015
> ### Title: Data from the hyperLOPIT technology on Mouse E14TG2a embryonic
> ### stem cells
> ### Aliases: hyperLOPIT2015 hyperLOPIT2015ms3r1 hyperLOPIT2015ms3r2
> ### hyperLOPIT2015ms3r3 hyperLOPIT2015ms2
> ### Keywords: datasets
>
> ### ** Examples
>
> data(hyperLOPIT2015)
> hyperLOPIT2015
MSnSet (storageMode: lockedEnvironment)
assayData: 5032 features, 20 samples
element names: exprs
protocolData: none
phenoData
sampleNames: X126.rep1 X127N.rep1 ... X131.rep2 (20 total)
varLabels: Replicate TMT.Reagent ... Fraction.No (6 total)
varMetadata: labelDescription
featureData
featureNames: Q9JHU4 Q9QXS1-3 ... Q9Z2R6 (5032 total)
fvarLabels: entry.name protein.description ... cell.surface.proteins
(24 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
- - - Processing information - - -
Loaded on Thu Nov 5 18:07:10 2015.
Normalised to sum of intensities.
MSnbase version: 1.19.3
> pData(hyperLOPIT2015)
Replicate TMT.Reagent Acquisiton.Method Gradient.Fraction
X126.rep1 1 X126 MS3 Cytosol
X127N.rep1 1 X127N MS3 1 to 6 (pooled)
X127C.rep1 1 X127C MS3 8 to 9 (pooled)
X128N.rep1 1 X128N MS3 10 to 11 (pooled)
X128C.rep1 1 X128C MS3 12
X129N.rep1 1 X129N MS3 14
X129C.rep1 1 X129C MS3 16
X130N.rep1 1 X130N MS3 18
X130C.rep1 1 X130C MS3 Chromatin
X131.rep1 1 X131 MS3 19
X126.rep2 2 X126 MS3 Cytosol
X127N.rep2 2 X127N MS3 1 to 6 (pooled)
X127C.rep2 2 X127C MS3 7 to 9 (pooled)
X128N.rep2 2 X128N MS3 10 to 11 (pooled)
X128C.rep2 2 X128C MS3 12
X129N.rep2 2 X129N MS3 14 to 15 (pooled)
X129C.rep2 2 X129C MS3 17
X130N.rep2 2 X130N MS3 18 to 19 (pooled)
X130C.rep2 2 X130C MS3 Chromatin
X131.rep2 2 X131 MS3 20
Iodixonal.Density Fraction.No
X126.rep1 0.0 1
X127N.rep1 6.0 2
X127C.rep1 11.0 3
X128N.rep1 13.3 4
X128C.rep1 14.6 5
X129N.rep1 17.4 6
X129C.rep1 20.1 7
X130N.rep1 26.8 8
X130C.rep1 NA 10
X131.rep1 34.5 9
X126.rep2 0.0 1
X127N.rep2 5.2 2
X127C.rep2 10.0 3
X128N.rep2 12.5 4
X128C.rep2 14.0 5
X129N.rep2 17.3 6
X129C.rep2 20.9 7
X130N.rep2 24.7 8
X130C.rep2 NA 10
X131.rep2 31.9 9
> head(exprs(hyperLOPIT2015))
X126.rep1 X127N.rep1 X127C.rep1 X128N.rep1 X128C.rep1 X129N.rep1
Q9JHU4 0.028 0.034 0.024 0.014 0.026 0.045
Q9QXS1-3 0.039 0.134 0.095 0.053 0.084 0.121
Q9ERU9 0.021 0.013 0.014 0.009 0.024 0.054
P26039 0.120 0.255 0.148 0.091 0.135 0.095
Q8BTM8 0.055 0.139 0.078 0.050 0.077 0.098
A2ARV4 0.000 0.085 0.223 0.166 0.292 0.107
X129C.rep1 X130N.rep1 X130C.rep1 X131.rep1 X126.rep2 X127N.rep2
Q9JHU4 0.107 0.341 0.059 0.321 0.037 0.064
Q9QXS1-3 0.107 0.128 0.122 0.117 0.033 0.073
Q9ERU9 0.116 0.257 0.209 0.284 0.026 0.017
P26039 0.041 0.057 0.014 0.043 0.111 0.181
Q8BTM8 0.093 0.171 0.079 0.160 0.062 0.108
A2ARV4 0.041 0.051 0.000 0.036 0.003 0.054
X127C.rep2 X128N.rep2 X128C.rep2 X129N.rep2 X129C.rep2 X130N.rep2
Q9JHU4 0.058 0.059 0.067 0.078 0.140 0.208
Q9QXS1-3 0.074 0.062 0.081 0.142 0.190 0.069
Q9ERU9 0.023 0.029 0.039 0.071 0.105 0.171
P26039 0.141 0.144 0.152 0.119 0.075 0.028
Q8BTM8 0.091 0.086 0.099 0.111 0.117 0.095
A2ARV4 0.147 0.257 0.291 0.143 0.064 0.028
X130C.rep2 X131.rep2
Q9JHU4 0.141 0.147
Q9QXS1-3 0.151 0.125
Q9ERU9 0.304 0.215
P26039 0.017 0.033
Q8BTM8 0.144 0.087
A2ARV4 0.005 0.008
>
>
>
>
>
> dev.off()
null device
1
>
|
Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and