Scatter Plot from Scientific Research

Example of the effect of principal components (PC) removal on the detection of a CNV, using PCA or LOO-PCA. Plots indicate coverage for each target along a common DNA stretch. When no PC is removed, coverage (dotted line) of the CNV (in this case, a heterozygous deletion) falls into the normal range of variation of 10 control samples (gray area) and cannot be automatically detected. Removal of initial PC components reduces the noise linked to normal variation of coverage; however, when standard PCs removal is applied, it also reduces the amplitude of the true signal linked to the real CNV (top row). This is not the case for PC removal using the LOO-PCA approach, which reduces the noise associated with normal variation of coverage but does not affect the true signal (bottom row).

DOI