msms.spk: Yeast lisate samples spiked with human proteins

In msmsTests: LC-MS/MS Differential Expression Tests

Description

A MSnSet with a spectral counts in the expression matrix and a treatment factor in the phenoData slot.
The spectral counts matrix has samples in the columns, and proteins in the rows. Each sample consists in 500ng of standard yeast lisate spiked with 100, 200, 400 and 600fm of a mix of 48 equimolar human proteins (UPS1, Sigma-Aldrich). The dataset contains a different number of technical replicates of each sample.

Usage

data(msms.spk)

Format

A MSnSet

References

Josep Gregori, Laura Villareal, Alex Sanchez, Jose Baselga, Josep Villanueva (2013). An Effect Size Filter Improves the Reproducibility in Spectral Counting-based Comparative Proteomics. Journal of Proteomics, DOI http://dx.doi.org/10.1016/j.jprot.2013.05.030

Laurent Gatto and Kathryn S. Lilley, MSnbase - an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation, Bioinformatics 28(2), 288-289 (2012).

See Also

See MSnSet for detail on the class, and the exprs and pData accessors.

Examples

data(msms.spk)
msms.spk
dim(msms.spk)
table(pData(msms.spk))
head(exprs(msms.spk))

Example output

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, sd, var, xtabs

The following objects are masked from ‘package:base’:

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

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: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: ProtGenerics

Attaching package: ‘ProtGenerics’

The following object is masked from ‘package:stats’:

    smooth


This is MSnbase version 2.16.0 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: ‘MSnbase’

The following object is masked from ‘package:base’:

    trimws

Loading required package: msmsEDA
MSnSet (storageMode: lockedEnvironment)
assayData: 685 features, 19 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: Y500U100_001 Y500U100_002 ... Y500U600_006 (19 total)
  varLabels: treat
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
  pubMedIds: http://www.ncbi.nlm.nih.gov/pubmed/23770383 
Annotation:  
- - - Processing information - - -
 MSnbase version: 1.8.0 
[1] 685  19

U100 U200 U400 U600 
   4    6    3    6 
        Y500U100_001 Y500U100_002 Y500U100_003 Y500U100_004 Y500U200_001
YKL060C          151          195          188          184          221
YDR155C          154          244          237          232          190
YOL086C           64           89          128          109          116
YJR104C          161          155          158          172          164
YGR192C          157          161          173          175          177
YLR150W           96          109          113          115          119
        Y500U200_002 Y500U200_003 Y500U200_004 Y500U200_010 Y500U200_011
YKL060C          201          187          194          325          272
YDR155C          187          215          189          215          194
YOL086C          119          139          114          271          141
YJR104C          165          161          184          272          164
YGR192C          164          176          174          167          179
YLR150W          121          141          124          145          153
        Y500U400_002 Y500U400_003 Y500U400_004 Y500U600_001 Y500U600_002
YKL060C          149          153          104          275          259
YDR155C          147          150          138          177          174
YOL086C          146          165          140          218          214
YJR104C          100           98           98          248          241
YGR192C           96          110           96          140          145
YLR150W           95          109           78          120          125
        Y500U600_003 Y500U600_004 Y500U600_005 Y500U600_006
YKL060C          302          294          229          238
YDR155C          197          193          178          183
YOL086C          189          179          227          221
YJR104C          186          192          147          152
YGR192C          131          132          148          145
YLR150W          120          111          108          115

msmsTests documentation built on Nov. 8, 2020, 5:25 p.m.