  Different approaches have been adopted to study short- and long-term stellar
magnetic activity, and although the mechanisms by which low-mass stars generate
large-scale magnetic fields are not well understood, it is known that stellar
rotation plays a key role. There are stars that show a cyclical behaviour in
their activity which can be explained by solar dynamo or $\alpha\Omega$ dynamo
models. However, when studying late-type dwarf stars, it is necessary to
implement other indicators to analyse their magnetic activity. In the present
work, we perform a comparative study between the best-known activity indicators
so far defined from the Ca II and H$\alpha$ lines to analyse M-dwarf stars. We
studied a sample of 29 M stars with different chromospheric activity levels and
spectral classes ranging from dM0 to dM6. To do so, we employed 1796 wide range
spectra from different instruments with a median time span of observations of
21 yr. In addition, we complemented our data with photometric observations from
the TESS space mission for better stellar characterisation and short-term
analysis. We obtained a good and significant correlation ($rho = 0.91$) between
the indexes defined from the two lines for the whole set of stars in the
sample. However, we found that there is a deviation for faster rotators (with
$P_{rot} < 4$ days) and higher flare activity (at least one flare per day).
There is an overall positive correlation between Ca II and H$\alpha$ emission
in dM stars, except during flare events. In particular, we found that
low-energy high-frequency flares could be responsible for the deviation in the
linear trend in fast-rotator M dwarfs. This implies that the rotation period
could be a fundamental parameter to study the stellar activity and that the
rotation could drive the magnetic dynamo in low-mass active stars.
