ATRAC VS MP3PRO
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If it's not settled yet, I think the arguments for Atrac3+ and against Mp3Pro are pretty solid. I vote for Atrac3+ as well.
ATRAC encoder
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However, I think somebody should really test whether the best (Sony) hardware Atrac encoders are _different_ from the latest SonicStage software release (assuming same version of Atrac now).
It's all very fine to assume there are no differences, but that's not a proof in scientific terms and it leaves way too much room for useless idle speculation, which is going to be rampant anyhow.
Maybe somebody with connections to the Atrac3 forum people could encourage a user there to encode a few tracks both with a hardware encoder and Sonicstage and see if they are bit-accurate?
Then again, even if we'd find out that hardware encoders are different in their output, it still doesn't solve the question of which encoder to use.
As such, for the sake of implementation easiness I recommend going with the encoder that the person doing the encoding is most comfortable using.
If somebody complains, we can ask him/her to conduct her own tests.
ANCHORS
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As for anchors, I think they should be of clearly higher/lower quality in many respects.
Remember, this is a subjective analysis and some people find some artifacts annoying, while other people are almost ignorant of them.
That is, making the anchors too difficult to spot will only muddy the results.
Bitrate bloat (esp. WMA Std)
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I know this issue is not a favourite amongst many of us, but how will the bit-rate averaging issue be handled?
While a 5-25% difference in avg bitrate may not always be critical at 128-160kbps, it can have serious skewing at 64 kbps testing, no?
I for one have noticed in my own testing that getting WMA 9.1 Standard 2-pass VBR (ABR) to achieve anywhere near the advertised bitrate is really hard, considering there isn't much flexibility in choosing the target bitrates.
For example, I'm now encoding to 128 ABR for a test of mine and WMA9 constantly gives 140-160 ABR on most tracks, even though the target is set to 128 kbps (2-pass vbr, 9.1 WMA std, encoded from dbPowerAMP rel.11).
Can this issue be handled in any meaningful manner? Is it a problem with the chosen sample set?
BTW, the problem of average bitrate fluctuation with OGG (aotuv b3) and MP3 (lame 3.96.1) is of much smaller magnitude - at least on my encodings.
SOFTWARE
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What software will be (can be used) to conduct the test when the testers download the sample pack?
I'm not very fond of ABCHR Java version myself.
Also, this is probably a FAQ, but I couldn't find an answer for this by searching, how will the samples be decoded into the final test form (in regards to clipping, gain/limiting, dither)?
CHECKING
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Would it be possible to check the test data submissions for accidental clicks?
For example, if for a certain sample set both samples are rated below 5.0, this is more than likely a mistake. It wouldn't be too difficult to check for this, if it's not already checked for.
I have had this happen to me on various occasions during the previous test (when clicking play/stop buttons and moving sliders): i'd rate a sample that I had ABXed properly at say 3.5. However, I had accidentally also moved the paired sample rating to 4.8 without noticing it.
Other than that, my hat goes to you on staring to pull this test together. It's not easy work, but somebody's gotta do it

regards,
Halcyon
PS I hope you recover soon from you operation. Take it easy though. Health is more important than testing