Galaxy |

MSI classification (version 1.10.0.0)

Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData:

Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)

Is the input file a processed imzML file :

Analysis step to perform:

Select the method for classification:

Crossvalidation or analysis:

The number of PLS components:

Multiple values are allowed (e.g. 1,2,3 or 2:5)

Define the fold variable:

Name of the pData slot where fold is stored:

each fold must contain pixels of all categories

Define the response variable y:

Name of the pData slot where y is stored:

Outputs of MSI_combine tool have 'combined_sample' as name

Results as .RData output:

Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. More information on Cardinal

This tool provides three different Cardinal functions for supervised classification of mass-spectrometry imaging data.

Input data: 3 types of input data can be used:

imzml file (upload imzml and ibd file via the "composite" function) Introduction to the imzml format
Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)

Options:

PLS(-DA): partial least square (discriminant analysis)
O-PLS(-DA): Orthogonal partial least squares (discriminant analysis)
Spatial shrunken centroids

Output:

Pdf with the heatmaps and plots for the classification
Tabular file with information on masses and pixels: toplabels/classes (PLS, spatial shrunken centroids)
optional RData output to further explore the results with Cardinal in R