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ahmohamed / lipidr

Data Mining and Analysis of Lipidomics datasets in R
https://www.lipidr.org/
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mva function issue #12

Closed Lucianabarros closed 4 years ago

Lucianabarros commented 4 years ago

Hello,

great code! But mva() is not working properly for method = "PCA". It got a warning and did not work.

Warning messages: 1: 'info.txtC = NULL' argument value is deprecated; use 'info.txtC = 'none'' instead. 2: 'fig.pdfC = NULL' argument value is deprecated; use 'fig.pdfC = 'none'' instead.

Thanks!

Luciana

ahmohamed commented 4 years ago

Hi @Lucianabarros,

Thanks for your interest in lipidr. Please ignore the warning, since this is because of changes in ropls package, and it's kept intentionally for backward compatibility. They will be probably be fixed in the next release.

Can you double check that the method did not work? You should get an Error if the method failed to run. If you can provide the error, I can look into why this is happening.

Ideally, can you follow the example here (https://www.lipidr.org/reference/mva.html) and see if you can reproduce the plot:

mvaresults <- mva(data_normalized, measure = "Area", method = "PCA")
plot_mva(mvaresults, color_by = "group")

Cheers. Ahmed.

ahmohamed commented 4 years ago

@Lucianabarros Let me know if the issue was resolved so I can help or close the issue here.

Lucianabarros commented 3 years ago

Sorry for the delayed response. It works on other dataset. Maybe is some issue with the data. Thank you!