Spike-in ChIP-chip data set

Description

This data set is part of a quality control study for tiling microarrays (Johnson et al., 2008), in which spike-ins were used to assess the influence of microarray platforms, preparation procedures, and analysis algorithms on the accuracy and reproducibility of ChIP-chip experiments. Here, the expression intensities of one region from the 'undiluted' data set investigated with Affymetrix arrays is selected, consisting of 452 probes and two conditions with three replicates each. The data has been normalized using quantile normalization and probe positions remapped to a common reference.

Usage

data(spikeInData)

Format

exprs

Matrix with expression intensities, with rows representing probes and columns arrays. The names of the rows and columns contain the probe position and the treatment, respectively.

pval

Vector with p-values assessing the differential effect between the conditions with a modified t-test. For details, please see the vignette of this package.

reference

Data frame containing the location of the spike-in.

Source

GEO accession IDs: GSM248996, ..., GSM249001

References

Johnson, D. S. et al. (2008). Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Research, 18(3):393-403.

Results