Evaluation of data analysis platforms and compatibility with MALDI-TOF imaging mass spectrometry datasets
R code for processing done using Cardinal on Pseudomonas aeruginosa PA14 imaging mass spectrometry data sets. Cardinal 2.4.0.9000, a forked branch of Cardinal MSI with several pending bug fixes, can be found here. Discussion with the developer regarding the bug fixes in Cardinal 2.4.0.9000 is currently ongoing and will be updated on this page. Custom in-house functions used during analysis can be found in the cardinalscripts repository.
R scripts for any statistical analysis done on individual or combined data sets.
R scripts used to generate ion/segmentation images for publication. Further editing done in Inkscape.
Spot Lists from Bruker FlexImaging v4.1 and ROI CSV tables used for analysis.
o Fix bug in 'spatialFastmap()' when iterating over
FastMap components where
'iData(x)[,spatial$neighbors[[oa]]]' and
'iData(x)[,spatial$neighbors[[ob]]]' are stored
as a numeric vector instead of a matrix
o Fix bug in 'spatialShrunkenCentroids()' where
'if ( all(class==pred$class) )' causes error
due to NA values in 'class' or 'pred$class'