Although wPCA has been used successfully to reduce the noise of STEM-EDX data , there are challenging situations in practice where wPCA fails to extract meaningful signals from noisy data with low X-ray counts, as we will demonstrate using an SiC metal-oxide-semiconductor field-effect transistor (MOSFET) sample composed of silicon (Si), silicon oxide (SiO 2 ), and silicon carbide (SiC) (Figure ). The difficulties are as follows. First, as suggested in existing work , the rescaling factors G and H used in applying wPCA should be estimated from the noisy data itself, but the estimate deteriorates under the high noise level, and especially near-zero intensities that typically appear in EDX data. Second, the spectra of different compositions often correlate each other; in our experiment, the spectral signatures from the SiC and Si phases are close to each other, with C-peaks typically being much smaller than Si-peaks. As a result, we only have the signatures of SiC and SiO 2 extracted by the direct application of wPCA, and cannot have the pure signature of Si.