Hello everyone,
We are using MetaboAnalyst for Volcano differential analyses.
As a test, we loaded a file with “samples in column”, and the exact same file transposed, using “samples in raw”. The number of samples, features, groups detected by “Data check” was exactly the same in both cases. We performed the same normalisation process in both files. But the results obtained in the Volcano analysis was clearly different … with more down-regulated features highlighted using the ‘samples in row’ file.
Have you ever noticed this strange result? What could be the cause?
Thanks, best regards.