Batch effect correction when multiple sequencing platforms are used

JF James H. R. Farmery
MS Mike L. Smith
AL Andy G. Lynch
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Our observation has been that estimates from the HiSeqX platform are shorter on average than estimates from the HiSeq. 2000 platform. We have also observed that samples sequenced on the HiSeqX platform show lower scores in quality assessment. To account for this effect we propose that a mean correction should be applied to estimates from the HiSeqX platform.

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