Hi forum,

I wonder if it is possible to discuss how to use MetaboAnalyst with spatial metabolomics data.

The main difference for spatial analysis is that for each pixel in a sample, we have a list of metbolites with their intensities; instead of one list of metabolites for each sample.

I tried to do the statistical analysis on intensities data that have been normalized within each sample (that is, there is still batch effects across samples). SanityCheckData returns this (btw, I really like this function):

[1] “A total of 1913 groups found with 165574 samples.”

[1] “At least **two** groups and **three replicates** per group are required for analysis!”

[1] “It seems the number of groups is big. Make sure to specify the correct format (i.e. samples in **columns** or **rows**) in the Data Upload page”

I know 165574 samples are actually my samples (16) * #pixels.

But I am not too sure what is the 1913 groups…

I have 156 metabolites.

And I defintely do not have sample triplicates…

Any insight would be super helpful! I know spatial is quite new and there is not much info circling around…

Thank you so much!