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MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

Zhen Shao12, Yijing Zhang3, Guo-Cheng Yuan1, Stuart H Orkin124* and David J Waxman3*

Author Affiliations

1 Departments of Pediatric Oncology and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA

2 Division of Pediatric Hematology-Oncology, The Karp Family Research Laboratories, Children's Hospital, 300 Longwood Ave, Boston, MA 02115, USA

3 Division of Cell and Molecular Biology, Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215, USA

4 Harvard Stem Cell Institute and the Howard Hughes Medical Institute, 1 Blackfan Circle, Karp Research Building, Children's Hospital, Boston, MA 02115, USA

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Genome Biology 2012, 13:R16  doi:10.1186/gb-2012-13-3-r16

Published: 16 March 2012

Additional files

Additional file 1:

MAnorm package written in MATLAB and R.

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Additional file 2:

Supplementary figures.

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Additional file 3:

Supplementary text. Includes text on the use of MAnorm normalized read density to determine whether the peak calling cutoff is comparable between two ChIP-seq data sets; results of downstream analyses following MAnorm are robust to different peak cutoffs; integrating multiple replicates in ChIP-seq data set comparison; derivation of the P-value that quantifies the significance of differential binding at peak regions; using MAnorm to compare H3K36me3 ChIP-seq data; assessing the effect of number of common peaks used in analysis; comparing signal-to-noise ratio before and after normalization; Supplementary Methods.

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Additional file 4:

Supplementary Tables - comparison of MAnorm with other methods.

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