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kuwisdelu / Cardinal

Mass spectrometry imaging toolbox
http://www.cardinalmsi.org
Artistic License 2.0
42 stars 14 forks source link

normalization is not processed #7

Closed DennisJakob closed 5 years ago

DennisJakob commented 5 years ago

Hi, I want to normalize imzml data with msi_TIC <- process(normalize(msi,method = "tic")) but it takes for ages. After all it stops with 35 warnings:

In serialize(data, node$con) : 'package:stats' may not be available when loading

Do you know where the problem is there?

kuwisdelu commented 5 years ago

If you are only getting warnings, does it complete and return a reasonable dataset?

The warning must be coming from the parallel worker sessions, but if there are no errors, it may not be affecting anything.

Depending on the size of your dataset, the overhead of parallelization may not be worth it.

You can try using register(SerialParam()) during your session or passing BPPARAM=SerialParam() to process() and see if running things serially is better.

DennisJakob commented 5 years ago

No it does not return a dataset.

I tried running it serially and it works fine! Thanks for the suggestion.