Metabolomics Society Forum

Software => XCMS Online => metaXCMS => Topic started by: gstacy on August 24, 2012, 01:03:30 PM

Title: Peak Data Insertion Problems-Please Try Lowering ppm Param
Post by: gstacy on August 24, 2012, 01:03:30 PM
Hello,

When I process my XCMS data for metaXCMS on the R platform I receive this message during feature detection "Peak Data Insertion Problems-Please Try Lowering ppm parameter".  While the process completes and I can move on to the next step, I am wondering what this means and if there is a way I can lower the ppm parameter that is currently set at 25 ppm.

Thank you,
Stacy
Title: Re: Peak Data Insertion Problems-Please Try Lowering ppm Par
Post by: Carsten on August 30, 2012, 02:35:46 AM
Hi Stacy,

the centWave algorithm has a two step feature detection framework.
The first step is the detection of connected centroids, which are called ROI (region of interest).
If within one scan the selection of a centroid is not distinct,
this could be caused by a too large search window (ppm parameter).

If you have not many warnings, you can safely ignore them.
If not, then you should lower your ppm parameter.

Carsten