[camera_annotate] Error in EIC generation about tools-metabolomics

[lecorguille]

NA values in xcmsSet. Use fillPeaks() on the object to fill-in missing peak values. Note however that this will also insert intensities of 0 for peaks that can not be filled in.

Did you try the option Replace the remain NA by 0 in the dataMatrix in xcms fillChromPeaks ?

[melpetera]

The thing is this option only concerns the dataMatrix output. Previously fillPeaks provided 0 values instead of NA I guess in the xcms object, but now with findCromPeaks when it is not able to fill the NA it leaves it as NA in the xcms object. This allows an iterative use of fillChromPeaks (which is cool), but it is a limitation for CAMERA's EIC that does not want to run if there are NA in the xcms object.

I guess we should ping the CAMERA R package developpers.

[yguitton]

Hi all,

A little up on that issue that seems to be link to the forum message https://community.france-bioinformatique.fr/t/probleme-creation-eic-camera/2722/2?u=yguitton

Did someone already found a way to deal with such error?
Best
Yann

[melpetera]

As the problem would be NA values, in fact there are at least two different ways to reformulate the problem:

• How to make CAMERA functions handle the NA-left condition?
• How to make the Rdata content compatible again with the no-NA policy of CAMERA?

I highlight that because maybe in the second case it would be possible to "just" add in the CAMERA Galaxy wrapper a step to convert NA to 0 in the xcms object in case the user ask for EIC? I am not very familiar with these object, but maybe it is something that could be manually replaced?