Johannes Rainer

If you know already IS or other landmark features it should be possible to feed them into the xcms peak group alignment. `PeakGroupsParam` has a parameter `peakGroupsMatrix` which allows to...

OK, I'll have a look into that.

Note that you are calling `findChromPeaks` twice on the same object, i.e. the `OnDiskMSnExp` object with the raw data. The error you are getting (which is indeed very cryptic) comes...

This is indeed strange. What is the output of ```r table(msLevel(raw_data1a)) ``` on your data? Could it be that you have some files in your data set with only MS1...

In addition, I would strongly suggest that you switch to the *new* functionality (see the xcms vignette for details), as we did also some improvement/changes especially in the new code...

Firstly, if you are using `xcmsSet`, `retcor` and `groupval` you are using the *old* xcms user interface and classes. In that case you don't have to use the `as(x, "xcmsSet")`...

There is no dedicated function available yet to transform intensity values - but it's definitely an important issue. I will think of a (flexible) solution.

I've now implemented a `transformIntensity` method for chromatographic data in the `MSnbase` and `xcms` packages. That function allows you to transform intensity values (along with peak data if you have...

Thanks @stanstrup , yes, sorry for that, but switching to the bleeding edge devel versions of the packages is not too simple.

Intersting! I will have a look if I too get that error...