Low rank matrix factorization is a fundamental building block in machine learning, used for instance to summarize gene expression profile data or word-document counts. To be robust to outliers and differences in scale across features, a matrix factorization step is usually preceded by ad-hoc feature normalization steps, such as tf-idf scaling or data whitening. We propose in this work to learn these normalization operators jointly with the factorization itself. More precisely, given a d*n matrix X of d features measured on n individuals, we propose to learn the parameters of quantile normalization operators that can operate row-wise on the values of X and/or of its factorization UV to improve the quality of the low-rank representation of X itself. This optimization is facilitated by the introduction of a differentiable quantile normalization operator built using optimal transport, providing new results on top of existing work by Cuturi et al (2019). We demonstrate the applicability of these techniques on synthetic and genomics datasets.