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!