Quantized correlation coefficient for measuring reproducibility of ChIP-chip data

Reproducibility of grouped data assessed by intraclass correlation coefficient - eAppendix

Here, μ represents the overall mean, βi is the deviation of respondent i from the overall mean, and εij is the deviation of i-th respondent’s reported value from his true value, μ+ βi, on occasion j. βi and εij are independent normal with mean 0 and variance σ β and σ , respectively. The intraclass correlation coefficient (ICC) ρ is calculated as share of between-class variability σ β in total ...

An integrated workflow for analysis of ChIP-chip data.

Although ChIP-chip is a powerful tool for genome-wide discovery of transcription factor target genes, the steps involving raw data analysis, identification of promoters, and correlation with binding sites are still laborious processes. Therefore, we report an integrated workflow for the analysis of promoter tiling arrays with the Genomatix ChipInspector system. We compare this tool with open-so...

Analyzing ChIP-chip Data Using Bioconductor

The interpretation of ChIP-chip data poses two computational challenges: first, what can be termed primary statistical analysis, which includes quality assessment, data normalization and transformation, and the calling of regions of interest; second, integrative bioinformatic analysis, which interprets the data in the context of existing genome annotation and of related experimental results obt...

ChIP-chip: data, model, and analysis.

ChIP-chip (or ChIP-on-chip) is a technology for isolation and identification of genomic sites occupied by specific DNA-binding proteins in living cells. The ChIP-chip signals can be obtained over the whole genome by tiling arrays, where a peak shape is generally observed around a protein-binding site. In this article, we describe the ChIP-chip process and present a probability model for ChIP-ch...

Supplement: Analyzing ChIP-chip data using Bioconductor