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We investigate the cold nuclear matter effects on $J/\psi$ production, whoseunderstanding is fundamental to study the quark-gluon plasma. Two of theseeffects are of particular relevance: the shadowing of the parton distributionsand the nuclear absorption of the $c\bar{c}$ pair. If $J/\psi$'s are notproduced {\it via} a $2 \to 1$ process as suggested by recent theoreticalworks, one has to modify accordingly the way to compute the nuclear shadowing.This naturally induces differences in the absorption cross-section fit to thedata. A careful analysis of these differences however requires taking intoaccount the experimental uncertainties and their correlations, as done in thiswork for $d$Au collisions at $\sqrtsNN=200\mathrm{GeV}$, using severalshadowing parametrisations.

On the theoretical and experimental uncertainties in the extraction of the J/psi absorption cross section in cold nuclear matter