"Frances the Mute" is comparable to The Mars Volta's 2003 release "De-Loused in the Comatorium", with its cryptic lyrics and highly layered instrumentals, although the progressive rock influence is stronger on "Frances the Mute" than it was on "De-Loused in the Comatorium". "The Widow" is notably the only short, pop-structured song on the album, although the last half of it features a lengthy, non-radio-friendly outro of manipulated tape loops of organs and electronic noise; for the single release, this part was edited out. Ambient noise plays a larger role on "Frances the Mute" than it does on "De-Loused in the Comatorium": "Cygnus...Vismund Cygnus" ends with the recording of children's voices and passing cars (made by Omar Rodriguez-Lopez in front of the house where he used to live with Bixler-Zavala and Ward), while the first movement of "Miranda That Ghost Just Isn't Holy Anymore" ("Vade Mecum") features 4 minutes of coquí frogs (credited as "The Coquí of Puerto Rico" on the album sleeve) singing while a thick soundscape is slowly built from guitars, synthesizers and Bixler-Zavala's voice.