There are several ways to physically transpose notes.
In the Score Editor or the Piano Roll Editor select the note (by double-clicking, control-clicking or dragging the mouse) and then choose Transpose, Shift or Octave from the Edit menu. Transpose moves the note by semitones. Shift moves the note in key and Octave moves the note up or down a number of octaves.
In the Score Editor or the Piano Roll Editor, choose the NS tool, select the note to be transposed by clicking and holding down the mouse over the note, and then drag the note up and down with the mouse. In the Score Editor this moves the note in key. In the Piano Roll Editor this moves the note by semitones. In the Score Editor, while the note is selected by holding the mouse button down over the note, you can move the note by semitones by pressing the Up or Down arrow keys on your computer keyboard.
Do not try to transpose a note by selecting the note and choosing Enharmonic Spelling from the Edit menu - this will only change the enharmonic spelling of the selected note.