Add selection box for PSM-level normalisation

[jgriss]

• Allow users to set the used PSM level normalization
• This is currently hard-coded to "center.median"
• Possible values (in MSnbase) are:
  • max
  • sum
  • quantiles
  • quantiles.robust
  • center.mean
  • center.median

[jgriss]

Note: max and sum work on the features (= rows) while the others work on the columns. It might be worth testing whether it's sensible to combine the two.

[jgriss]

@veitveit Based on the benchmarks center.median seems to be working best.

To keep the protocol simple, we might also just not add this parameter.

Alternatively, we could add an "advanced parameters" section. What do you think?

In any case, I'm scheduling this for the version after the next one.

[veitveit]

voting for keeping things simple Am Mi., 3. Okt. 2018 um 11:02 Uhr schrieb Johannes Griss < notifications@github.com>:

…

@veitveit <https://github.com/veitveit> Based on the benchmarks center.median seems to be working best. To keep the protocol simple, we might also just not add this parameter. Alternatively, we could add an "advanced parameters" section. What do you think? In any case, I'm scheduling this for the version after the next one. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#75 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APEZhWCteOgBb9pS9U0c8hRpvALPTaD3ks5uhH0ggaJpZM4W7ZJT> .

-- \|||/ (o o) ----ooO-(_)-Ooo---- Don't worry about life; you're not going to survive it anyway. http://computproteomics.bmb.sdu.dk

[jgriss]

Agreed. Let's not add this parameter.