Data matrices were constructed so that each row corresponded to a sample and each column represented the spectra datum at a given wavenumber, after processing as described in the previous section. The spectra pretreatment steps that provided a satisfactory

level of discrimination between defective and non-defective coffees were the following: (0) no additional treatment of raw data, (1) mean centering, (2) normalization and (4) first derivatives. Pretreatments (3) and (5), baseline correction and second derivatives, did not provide satisfactory separation between defective and non-defective coffees. Furthermore, baseline correction (3) provided undesirable separation by roasting temperature. The Ion Channel Ligand Library in vivo Protease Inhibitor Library high throughput scatter plots obtained by PCA analysis are displayed in Fig. 3. A clear separation between categories can be observed, with four distinct major groups: non-defective ( ), black ( ), dark ( ) and

light sour ( ), with some outlier points. The few outlier samples from each group that were present in other classes (for example, a few non-defective and black beans in the light sour group) correspond to samples subjected to extreme roasting conditions (light roast/lower temperature and dark roast/higher temperature). Regardless of the employed spectra processing technique, immature beans ( ) are somewhat scattered between light and dark sour defects. Clustering of immature and sour defects was also observed in the O-methylated flavonoid analysis of green coffees by ESI (+)-MS profiles (Mendonça et al., 2008) or DRIFTS (Craig et al., 2011), whereas Mancha Agresti et al. (2008) reported grouping of immature and black roasted coffee beans according to their volatile profiles. A clear separation between non-defective and defective coffee beans can be observed in all the plots displayed in Fig. 3. Evaluation of the loadings plots obtained after PCA analysis of raw and processed spectra (not shown) indicated that the spectral ranges that presented the highest influence on PC1 and PC2 values in association with the non-defective coffees

(PC1 and PC2 positive for spectra without further treatment, PC1 and PC2 negative for spectra submitted to mean centering, and PC1 negative and PC2 positive for normalized spectra) were the following: 1700–1500 and 970–600 cm−1, in general representing the regions in which non-defective coffees presented higher absorbance intensity in comparison to all defective categories (see Fig. 1). Loadings obtained for first derivatives could not be associated to specific regions in the spectra. Results from the principal components analysis indicate that the obtained spectra could provide enough information to develop classification models for non-defective and each specific class of defective roasted coffees.