We're comparing a histone modification in control samples vs. experimental samples in which the modifying enzyme is overexpressed. Western blotting indicates ~3X increase in the amount of modified histones, and qPCR of ChIPed material shows a similar increase for known target sites. Comparison of ChIP-Seq data sets indicate that the distribution of the modification is unchanged (i.e., the same peaks are detected in control and experiment). This result was anticipated by other experiments, so nothing earth-shattering.
The question: what is the appropriate method/algorithm for normalizing the ChIP-Seq data that demonstrates the enrichment we observe at these identical peaks? Most of the available tools seem designed for detecting different peaks, using the same (normalized) number of reads. In our case, however, such normalization essentially suppresses the difference in magnitude we detect by the other methods.
I'd appreciate suggestions from the more statistically-savvy members of the community.
Thanks,
Harold
The question: what is the appropriate method/algorithm for normalizing the ChIP-Seq data that demonstrates the enrichment we observe at these identical peaks? Most of the available tools seem designed for detecting different peaks, using the same (normalized) number of reads. In our case, however, such normalization essentially suppresses the difference in magnitude we detect by the other methods.
I'd appreciate suggestions from the more statistically-savvy members of the community.
Thanks,
Harold
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