Significant features designation

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Significant features designation

July 28, 2014, 12:49:41 PM

My XCMS online output has detected many features with p < 0.05 and a fold change of 2 or higher. I've checked the statistics tab in the parameter methods and confirmed that these features should be identified as significant based on the p-values and fold changes, however, the output is not recognizing these features as significant. Are there any other requirements for a feature to be identified as significant? Initially, I modified the HPLC/Orbitrap II parameters, and I've tried again using the default HPLC/Orbitrap II and received the same output. I have noticed a very small number of features in the feature list that have been identified as significant.

Re: Significant features designation

Reply #1 – August 15, 2014, 02:06:36 PM

Danielle,

I'm not sure that I understand. The features are significant when they the p-value, for that individual feature, falls below the designated alpha value in the statistics tab. However, regardless of this all detected features (with the exception of the features removed by minfrac) will appear in the results table. Features that are significant will have EIC, boxplots and spectral plots. If you are not seeing these please submit an error report via the xcmsonline contact page.

Cheers,

Paul