LPSeset: ExpressionSet for Testing PLGEM

In plgem: Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)

Description

This ExpressionSet object contains a subset of the microarray data used in References for PLGEM set-up and validation. Briefly, it contains normalized gene expression values from a total of 6 hybridizations on MG-U74Av2 Affymetrix GeneChip microarrays. Two experimental conditions are represented in this dataset: the baseline condition (‘C’) contains data of immature murine dendritic cells (4 replicates); the other condition (‘LPS’) contains data of the same cells stimulated for 4 hours with LPS (2 replicates).

Usage

  data(LPSeset)

Format

An object of class ExpressionSet.

Author(s)

Mattia Pelizzola [e-mail]

Norman Pavelka [e-mail]

References

Pavelka N, Pelizzola M, Vizzardelli C, Capozzoli M, Splendiani A, Granucci F, Ricciardi-Castagnoli P. A power law global error model for the identification of differentially expressed genes in microarray data. BMC Bioinformatics. 2004 Dec 17;5:203.; http://www.biomedcentral.com/1471-2105/5/203

Examples

  data(LPSeset)
  library(Biobase)
  head(exprs(LPSeset))

Example output

Welcome to plgem version 1.48.0 

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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

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

            C1   C2   C3   C4 LPS1 LPS2
100001_at  2.6  1.6  0.7  1.4  4.4  1.3
100002_at  8.8  8.0  9.2  3.4  7.0  1.4
100003_at 29.8 20.7 36.5 28.8  0.9  1.5
100004_at 49.1 51.9 49.6 45.5 36.2 38.3
100005_at 62.4 47.7 48.0 49.7 69.9 51.7
100006_at  0.5  4.1  5.3  2.1  6.4  0.9

plgem documentation built on Nov. 8, 2020, 5:31 p.m.