In the Laghu-bhāgavatāmṛta, Śrīla Rūpa Gosvāmī, commenting upon the Lord's transcendental position beyond the material qualities, says that Viṣṇu, as the controller and superintendent of material nature, has a connection with the material qualities. That connection is called yoga. However, the person who directs a prison is not also a prisoner. Similarly, although the Supreme Personality of Godhead Viṣṇu directs or supervises the qualitative nature, He has no connection with the material modes of nature. The expansions of Lord Viṣṇu always retain their supremacy; they are never connected with the material qualities. One may argue that Mahā-Viṣṇu cannot have any connection with the material qualities, because if He were so connected, Śrīmad-Bhāgavatam would not state that material nature, ashamed of her thankless task of acting to induce the living entities to become averse to the Supreme Lord, remains behind the Lord in shyness. In answer to this argument, it may be said that the word guṇa means “regulation.” Lord Viṣṇu, Lord Brahmā and Lord Śiva are situated within this universe as the directors of the three modes, and their connection with the modes is known as yoga. This does not indicate, however, that these personalities are bound by the qualities of nature. Lord Viṣṇu specifically is always the controller of the three qualities. There is no question of His coming under their control.
Although the causal and element-supplying features exist in material nature by dint of the glance of the Supreme Personality of Godhead, the Lord is never affected by glancing over the material qualities. By the will of the Supreme Lord the different qualitative changes in the material world take place, but there is no possibility of material affection, change or contamination for Lord Viṣṇu.