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sgibb / MALDIquant

Quantitative Analysis of Mass Spectrometry Data
https://strimmerlab.github.io/software/maldiquant/
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Averaging warping functions - plate by plate effect #67

Closed SamGG closed 3 years ago

SamGG commented 3 years ago

Hi, We are running analysis of patients. Samples need to be processed on the sampling day. So about 10 samples are acquired everyday in quadruplicate. Samples are profiled in linear mode. To correct day to day m/z variation, an aliquot of a reference mix is deposited on each plate in quadruplicate. We would like to warp each spectra of a plate using the 4 reference spectra. Currently the reference spectra of all the plates are pooled and a warping function is obtained for each spectra. This leads to 4 warping functions for each plate. How to average those and get one warping function? I am going to apply the 4 warping functions and average the resulting masses. I am wondering if there is a better/straight way. Best.

sgibb commented 3 years ago

Could you not use averageMassSpectra on the reference spectra and use this average spectrum for warping instead? Or use the closest (on the plate) reference spectrum for the sample?

sgibb commented 3 years ago

@SamGG feel free to reopen if you are not satisfied with this solution