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Though debated, the existence of claimed large-scale anomalies in the CMB isnot totally dismissed. In parallel to the debate over their statisticalsignificance, recent work focussed on masks and secondary anisotropies aspotential sources of these anomalies. In this work we investigatesimultaneously the impact of the method used to account for masked regions andthe impact of the ISW effect, which is the large-scale secondary anisotropymost likely to affect the CMB anomalies. In this sense, our work is an updateof both Francis & Peacock 2010 and Kim et al. 2012. Our aim is to identifytrends in CMB data with different mask treatments. We reconstruct the ISWsignal due to 2MASS and NVSS galaxies. We account for missing data using thesparse inpainting technique of Abrial et al. 2008 and sparse inpainting of theCMB, LSS and ISW and find that it constitutes a bias-free reconstruction methodsuitable to study large-scale statistical isotropy and the ISW effect. We focuson three large-scale CMB anomalies: the low quadrupole, the quad/oct alignment,and the octopole planarity. After sparse inpainting, the low quadrupole becomesmore anomalous, whilst the quad/oct alignment becomes less anomalous. Thesignificance of the low quadrupole is unchanged after subtraction of the ISWeffect, while the trend is that the quad/oct alignment has reducedsignificance, yet other hypotheses remain possible as well (e.g. exoticphysics). Our results also suggest that both of these anomalies may be due tothe quadrupole alone. The octopole planarity significance is also reduced afterinpainting and after ISW subtraction, however, we do not find that it was veryanomalous to start with. In the spirit of reproducible research, we make allcodes and resulting products which constitute main results of this paper publichere: http://www.cosmostat.org/anomaliesCMB.html.

Removal of two large scale Cosmic Microwave Background anomalies after subtraction of the Integrated Sachs Wolfe effect