Environmental differences in the stellar populations of early-type galaxies are explored using principal component analysis (PCA), focusing on differences between elliptical galaxies in Hickson Compact Groups (HCGs) and in the field. The method is model-independent and purely relies on variations between the observed spectra. The projections (PC1, PC2) of the observed spectra on the first and second principal components reveal a difference with respect to environment, with a wider range in PC1 and PC2 in the group sample. We define a spectral parameter (ζ ≡ 0.36PC1-PC2) which simplifies this result to a single number: field galaxies have a very similar value of ζ, whereas HCG galaxies span a wide range in this parameter. The segregation is found regardless of the way the input spectral energy distributions (SEDs) are presented to PCA (i.e. changing the spectral range; using uncalibrated data; subtracting the continuum or masking the SED to include only the Lick spectral regions). Simple models are applied to give physical meaning to the PCs. We obtain a strong correlation between the values of ζ and the mass fraction in younger stars, so that some group galaxies present a higher fraction of them, implying a more complex star formation history in groups. Regarding `dynamically related' observables such as a4 or velocity dispersion, we find a correlation with PC3, but not with either PC1 or PC2. PCA is more sensitive than other methods based on a direct analysis of observables such as the structure of the surface brightness profile or the equivalent width of absorption lines. The latter do not reveal any significant variation between field and compact group galaxies. Our results imply that the presence of young stars only amounts to a fraction of a per cent in its contribution to the total variance, reflecting the power of PCA as a tool to extract small variations in the spectra from unresolved stellar populations.