The solar quiet variation (Sq) observed at observatories near the latitude of the Sq vortex focus is difficult to assess because it is affected by both the geomagnetic activity level and the dynamics of the ionosphere and the upper atmosphere resulting in changes of the Sq ionospheric vortex shape and position. The use of only geomagnetically quiet days (QD) to calculate Sq for a given month can, to a certain extent, remove the effect of geomagnetic disturbances; however, the effect of the atmospheric dynamics still needs to be taken into account. The Sq vortex shape and position can be acquired from the horizontal vector of the geomagnetic field measured at geomagnetic observatories located in the European-African sector between 10ºN and 60ºN using vector rotation or calculating equivalent currents. Here we present results of a comparative analysis of two methods to extract Sq variations from the observations of the earth geomagnetic field. The analyzed data are measurements of the geomagnetic field done between 2007 and 2017 at the Coimbra Geomagnetic Observatory (COI, Portugal) located near 40ºN.The principal component analysis (PCA) based Sq curves are compared with the standard ones obtained using 5 international QD per month. For most of the analyzed years for the X component, the second PCA mode was identified as Sq variation whereas for the Y and Z components for all analyzed data sets the first PCA mode was identified as Sq variation. We studied differences and similarity of the PCA and IQD based Sq in relation to (1) the average geomagnetic activity level and (2) Sq vortex shape and position relatively to COI.