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Do codecs work differently on different MP3 players?

CNET's MP3 Insider blog has a great post on how the reviews team measures the audio response of MP3 players, and which ones come out on top. But I'm curious whether changing codecs changes the results.

CNET's MP3 Insider blog posted a fascinating entry the other day on how CNET Labs tests the audio response of different MP3 players. They load several files of the type that are used to test traditional stereo equipment, such as white noise and pure sine waves, then plays them back into an audio analyzer, which reports numbers for qualities such as signal-to-noise ratio and total harmonic distortion. Two Creative players come out on top, the iPod Classic in the middle, and Microsoft's Zune in seventh place due to fairly mediocre harmonic distortion scores.

Hardware isn't the only factor in how good an MP3 player sounds. Wikimedia Commons

As Donald Bell correctly points out, numbers lie: some of the best sounding MP3 players actually boost or depress certain frequencies to make up for the fact that you're probably listening to a digitally compressed file through a middling audio processor and cheap earbuds, with lots of ambient noise around you. (Good audio engineers tell you the same thing: level meters, for example, aren't the final arbiter of whether there's unacceptable distortion on a recording--your ears are.)

But putting aside the subjectivity of hearing, I'm curious about the effect of different codecs--the specific technology used to create a compressed digital sound file. Presumably, CNET Labs uses uncompressed WAV files to check the hardware. But I wonder if they've ever done tests--subjective or objective--of different types of compressed files against one another, like SoundExpert has done. I've long read that MP3 offers the lossiest compression, but is there a noticeable difference between AAC and Windows Media Audio (WMA) and Ogg at the same bitrate? And one step beyond that: does one player sound better with a particular codec than others?

Subjectively, I prefer WMA files over AAC files on my Zune. My iPods (a new Shuffle and fourth-generation 20GB unit) can't play WMA files, but when I convert those files to AAC using iTunes, they don't sound as good as the AAC files I rip from scratch, even though the converted files have a higher bitrate. MP3s don't sound as good as either AAC or fixed-bitrate WMA, but actually seem to sound better than variable-bitrate WMA. And MP3s seem to sound best on my fourth-generation iPod. Go figure.