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I know that Shiva, Durga, Vishnu, Surya and Ganesha are counted as manifestations of Nirguna brahman. Or in other way when nirguna brahman is seen through lens of maya, it is seen in 5 different ways. What I fail to make sense of is how come Vishnu is there in the list, but his wife is missing. Similarly, how same saguna brahman Shiva, Durga, Ganesha are related as husband , wife, son and then instead of another son Karthikeya we have Surya as fifth. I am also not able to make sense of the number 5 and one family having 3 saguna brahman. The thing is since all are manifestations of Nirguna brahman, there should be no hierarchy between each of them.

Can some explain logically how it is possible?

Since this question is about nirguNa brahman, I will answer this from the perspective of advaita. There is nothing special about the number five. Sri Shankara says in his Brahmasutra bhashya, that the supreme Lord can assume any form to bless his devotees. (BSB 1.1.20, see the quote below). There is no evidence from Sri Shankara's authentic works that he thinks there are only five forms of brahman.

http://www.sacred-texts.com/hin/sbe34/sbe34026.htm

With a beard bright as gold,' &c., cannot refer to the highest Lord, we reply that the highest Lord also may, when he pleases, assume a bodily shape formed of Mâyâ, in order to gratify thereby his devout worshippers. Thus Smriti also says, 'That thou seest me, O Nârada, is the Mâyâ emitted by me; do not then look on me as endowed with the qualities of all beings.'

Incidentally, the smriti in the above quote is Mahabharata, where Lord Narayana shows his cosmic form (vishwa roopa) to Narada.