A New Normalizing Algorithm for BAC CGH Arrays with Quality Control Metrics

<table>Intensity effect:  the estimated loess fit (red line) using the <svg height="16.6" id="M48" style="vertical-align:-3.50804pt" version="1.1" viewbox="0 0 59.862499 16.6" width="59.862499" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
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q-49 15 -74 55q-13 20 -11 42q56 21 88 61q-37 16 -62.5 51t-25.5 83q0 78 56.5 122t122.5 44h1q51 0 96 -27q71 4 136 15zM219 418q-34 0 -58 -32t-24 -87q0 -59 26.5 -96.5t67.5 -37.5q35 1 59 32t24 87q0 59 -26 96.5t-69 37.5zM241 -11q-62 0 -87 -21q-46 -39 -46 -78
q0 -41 38 -68.5t94 -27.5q69 0 106.5 31t37.5 80q0 52 -45 71q-33 13 -98 13z" id="x67"></path></g><g transform="matrix(.017,-0,0,-.017,29.47,12.162)"><path d="M649 676l-22 -187l-33 -2q3 56 -12 94q-8 20 -31.5 26.5t-86.5 6.5h-74l-90 -491q-4 -23 -6 -36.5t1 -25t7 -16.5t18 -9t27 -5t41 -3l-6 -28h-286l4 28q68 5 84 18.5t28 76.5l94 491h-55q-74 0 -100.5 -6t-41.5 -23q-24 -29 -54 -98l-32 1q32 98 53 188h22q7 -18 15 -22
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</svg> as the response with <svg height="16.6" id="M49" style="vertical-align:-3.50804pt" version="1.1" viewbox="0 0 70.387497 16.6" width="70.387497" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,12.162)"><path d="M238 0h-223v26q48 5 60 17t12 61v473q0 50 -10.5 60.5t-58.5 15.5v24q73 8 148 35v-608q0 -49 11.5 -61t60.5 -17v-26z" id="x6C"></path></g><g transform="matrix(.017,-0,0,-.017,4.363,12.162)"><path d="M257 449q92 0 154 -65t62 -158q0 -112 -67 -175t-150 -63q-98 0 -158.5 66.5t-60.5 154.5q0 59 21 106.5t54.5 75.5t71 43t73.5 15zM244 416q-48 0 -81 -47t-33 -128q0 -96 38 -158t99 -62q51 0 82 43.5t31 139.5q0 91 -36 151.5t-100 60.5z" id="x6F"></path></g><g transform="matrix(.017,-0,0,-.017,13.033,12.162)"><path d="M463 437l5 -8q-21 -38 -45 -51l-57 3q30 -35 30 -88q0 -76 -52.5 -118t-122.5 -42q-24 0 -51 5q-30 -21 -30 -42q0 -16 16 -27t47 -11q19 0 54 0.5t52 0.5q36 0 65.5 -8t53.5 -36t24 -74q0 -77 -75 -137.5t-174 -60.5q-79 0 -126 37.5t-48 84.5q0 32 24 56q21 21 83 70
q-49 15 -74 55q-13 20 -11 42q56 21 88 61q-37 16 -62.5 51t-25.5 83q0 78 56.5 122t122.5 44h1q51 0 96 -27q71 4 136 15zM219 418q-34 0 -58 -32t-24 -87q0 -59 26.5 -96.5t67.5 -37.5q35 1 59 32t24 87q0 59 -26 96.5t-69 37.5zM241 -11q-62 0 -87 -21q-46 -39 -46 -78
q0 -41 38 -68.5t94 -27.5q69 0 106.5 31t37.5 80q0 52 -45 71q-33 13 -98 13z" id="x67"></path></g><g transform="matrix(.017,-0,0,-.017,29.47,12.162)"><path d="M649 676l-22 -187l-33 -2q3 56 -12 94q-8 20 -31.5 26.5t-86.5 6.5h-74l-90 -491q-4 -23 -6 -36.5t1 -25t7 -16.5t18 -9t27 -5t41 -3l-6 -28h-286l4 28q68 5 84 18.5t28 76.5l94 491h-55q-74 0 -100.5 -6t-41.5 -23q-24 -29 -54 -98l-32 1q32 98 53 188h22q7 -18 15 -22
t37 -4h417q23 0 33.5 5t25.5 21h23z" id="x1D447"></path></g><g transform="matrix(.017,-0,0,-.017,44.582,12.162)"><path d="M528 54l-36 -38l-198 201l-198 -201l-36 38l197 200l-197 201l36 38l198 -202l198 202l36 -38l-197 -201z" id="xD7"></path></g><g transform="matrix(.017,-0,0,-.017,58.334,12.162)"><path d="M682 629q-1 -16 -1.5 -72t-2.5 -86l-31 -4q-5 92 -51 129t-139 37q-100 0 -177 -49t-116 -125t-39 -162q0 -122 66 -201t182 -79q83 0 137 42.5t112 128.5l26 -15q-12 -31 -42.5 -88t-45.5 -75q-139 -27 -199 -27q-148 0 -243 81.5t-95 226.5q0 173 129.5 274.5
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</svg> as the explanatory variable.</table>

BioMed Research International

fig2

Figure 2

Figure 2: A New Normalizing Algorithm for BAC CGH Arrays with Quality Control Metrics 