... - First of all, you can set `sep = ","` when exporting and `MSnSet` to a spreadsheet. Alternatively, you could also read the data in with `readMSnSet2` and set `sep = "\t"`.
- In `write.exprs`, you can define to also export the feature variables - you can provide feature variables one by one, of a ...
... You have two options.
1. Open your xlsx file with Excel and export it to csv, the use `readMSnSet2` to load it into R as an `MSnSet`
2. Import your xlsx file into R as a `data.frame` and use that `data.frame` as input to `readMSnSet2` to create an `MSnSet`
Have a look at `?readMSnSet2` or in the v ...
... It looks like there was a problem to access and download files from the PRIDE ftp server. Things seem to work on my end now:
> px1 <- PXDataset("PXD000001")
Object of class "PXDataset"
Id: PXD000001 with 12 files
 'F063721.dat' ...  ...
... From the dimensions of your 4 objects, I assume that the 10 sample (column) names are identical and that you want to combine along to features (rows). Could it be that `MSnset_Set4` has a feature that exists in a previous object? This would indeed lead to such an error. ...
... You can add a sequence (as a character) to plot to automatically annotate the plot. Below I have sp, an object of class Spectrum, and its sequence s:
Object of class "Spectrum2"
Retention time: 30:2
MSn level: 2
Peaks count: 121
Total ion count: 58841 ...
... SCX is strong cation exchange. I assume component here means 10 fractions that were then analysed my LC-MSMS.