Verse 6: And the LORD called yet again, Samuel. And Samuel arose and went to Eli, and said, Here am I; for thou didst call me. And he answered, I called not, my son; lie down again.
[He went forth to Eli] He did not run as previously, but proceeded more slowly and quietly; so that he might not wake the aged man, if he be sleeping and not calling. Thus prudence tempered the fervor of obedience (Mendoza).
Verse 7: Now Samuel (see Acts 19:2) did not yet know the LORD, neither was the word of the LORD yet revealed unto him (or, thus did Samuel before he knew the LORD, and before the word of the LORD was revealed unto him).
[He was not yet knowing the Lord] He was not accustomed to divine addresses; therefore, He did not know the voice of the Lord, nor His manner, of which He makes use when He addresses His prophets (Munster, similarly Vatablus, Lapide, Menochius, Malvenda, Tirinus). He did not know God with that acquaintance wherewith the prophets were wont, who have God as a familiar (Sanchez). Just as the Prophets are said to know God in the ultimate sense, when they enter into conversation more familiarly with God; so the prophets are not said to be ignorant of God, because they are destitute of that experimental knowledge, and of that ostensive illustration, as it were, which the Prophets have (Mendoza). He was not yet knowing the voice of Jehovah appearing and speaking; he was not yet knowing how to give an appropriate response to one addressing him. It is a Synecdoche of genus (Piscator). He was not knowing that the Lord speaks with His Prophets in such a quiet voice, which on account of this is called בַּת קוֹל, the Bath Kol, the daughter of the voice. Thus Maimonides (Grotius). But why Samuel, having been called by God, hastened to Eli, there is a twofold rationale of the divine providence. 1. So that he might be instructed concerning the manner in which he ought to prepare himself for the divine speech. 2. So that Eli, seeing him called by God, might have confidence in his sayings, as issuing from the oracle (Mendoza on verse 5). The יָדַע signifies to know something by experience; he had not yet experienced the Lord. Or perhaps it means this, that he was not differentiating between the voice of the Lord and of another. For to know is to discern, Jonah 4:11, who were not discerning between their right hand and their left hand. Or, he speaks of knowledge unique, or prophetic (Drusius). [Jonathan thus renders this whole passage: He had not yet learned to know instruction from before the Lord, and the word of the Lord’s prophecy was not yet manifested to him.]
Now Samuel did not yet know the LORD, etc.: Either, first, He was not acquainted with God in that extraordinary or prophetical way. Or rather, secondly, He did not yet understand, any more than before, that it was not Eli, but God, who spake to him. And this ignorance of Samuel’s served God’s design, that his simplicity might give Eli the better assurance of the truth of God’s call and message to Samuel.
Verse 8: And the LORD called Samuel again the third time. And he arose and went to Eli, and said, Here am I; for thou didst call me. And Eli perceived that the LORD had called the child.
He arose and went to Eli; he persists in the same readiness to obey and serve him and was not discouraged or driven from his duty by his double mistake and disappointment.
[And he says, Here am I] With the same words, wherewith he had presented himself the first and second time, he now presents himself the third time; he is no more upset, or impatient, because he, having been disappointed twice, is called a third time. Not so Peter. See John 21:15-17 (Mendoza).
[Therefore, Eli understood] Either by divine illumination, or rather by human reasoning (Mendoza, thus Lapide, Sanchez); for no one else was there, who might call him; and because Samuel was so pleasing to God (Lapide). Now, Eli had heard that of old God had spoken with holy men (Sanchez). But why did not Samuel understand that it was a divine calling? Response: Because Samuel was truly humble, who was supposing nothing lofty concerning himself. Whence he was thinking nothing less than that God was near to him, and was willing to communicate divine secrets with him (Mendoza).
Eli perceived, by the consideration of Samuel’s piety, of the sanctity of the place adjoining, from whence God had ofttimes spoken, and of the solitude of the place, where there was no human person besides himself who could or would have called Samuel in that manner.
 Hebrew: וַיֹּ֣סֶף יְהוָ֗ה קְרֹ֣א עוֹד֮ שְׁמוּאֵל֒ וַיָּ֤קָם שְׁמוּאֵל֙ וַיֵּ֣לֶךְ אֶל־עֵלִ֔י וַיֹּ֣אמֶר הִנְנִ֔י כִּ֥י קָרָ֖אתָ לִ֑י וַיֹּ֛אמֶר לֹֽא־קָרָ֥אתִי בְנִ֖י שׁ֥וּב שְׁכָֽב׃  Hebrew: וּשְׁמוּאֵ֕ל טֶ֖רֶם יָדַ֣ע אֶת־יְהוָ֑ה וְטֶ֛רֶם יִגָּלֶ֥ה אֵלָ֖יו דְּבַר־יְהוָֽה׃  Jonah 4:11: “And should not I spare Nineveh, that great city, wherein are more than sixscore thousand persons that cannot discern between their right hand and their left hand (לֹֽא־יָדַע֙ בֵּין־יְמִינ֣וֹ לִשְׂמֹאל֔וֹ); and also much cattle?”  Hebrew: וַיֹּ֙סֶף יְהוָ֥ה קְרֹא־שְׁמוּאֵל֮ בַּשְּׁלִשִׁית֒ וַיָּ֙קָם֙ וַיֵּ֣לֶךְ אֶל־עֵלִ֔י וַיֹּ֣אמֶר הִנְנִ֔י כִּ֥י קָרָ֖אתָ לִ֑י וַיָּ֣בֶן עֵלִ֔י כִּ֥י יְהוָ֖ה קֹרֵ֥א לַנָּֽעַר׃