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Archived Comments for: Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform

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  1. Author edits

    Jeanette Eckel-Passow, Mayo Clinic

    5 September 2011

    We would like to thank Henrik Bengtsson for his thorough review of our manuscript. Below we discuss some edits and clarification to our manuscript based on his review.

    1. CRMAv2 was the method used in the Aroma.Affymetrix software. Although this can be determined by reading Appendix 2, this was not directly stated in the manuscript.
    2. CRMAv2 does not apply an across-array normalization method. Thus, in the Results and Discussion section the following edits should be made:
    - Under the subsection, “Background correction”, the third sentence should read "Aroma.Affymetrix corrects for allelic crosstalk whereas CRLMM corrects for optical background and non-specific hybridization using a linear model after performing quantile normalization."
    - The “Across-array normalization” subsection should read, "Across-array normalization attempts to correct for systematic variability induced by array manufacturing, sample preparation, labeling, hybridization and scanning of the arrays [7]. By default, PennCNV, APT and CRLMM apply quantile normalization, which makes the distribution of probe intensities for each array equivalent [8]. Although these software apply quantile normalization, they utilize different target distributions. Particularly, APT utilizes the data at hand to define the target distribution, whereas PennCNV and CRLMM use the HapMap samples to define a target distribution. Although Aroma.Affymetrix does not apply quantile normalization, they do correct for probe sequence effects."
    - Likewise, the last sentence of subsection “Genomic-wave” should read, "Specifically, Aroma.Affymetrix corrects for GC content and PCR fragment length."
    - Similarly, Table 1 is incorrect. Under the Normalization column and Aroma.Affymetrix row, the cell should read, "Second, normalizes probe sequence effects."

    Competing interests