Hi everyone,
I have a difficult time deciding what the best way is to perform statistics on Mass Spec metabolomics data from two groups (Treatment and Control) run on 3 different days (3 biological replicates). Because of the different sensitivity of the machine each day, although the trend (or fold change) between Treatment and Control is similar, the raw peak area values differ from day to day so that if I plot the peak areas, the SD is high and the comparison becomes not statistically significant.
To account for the variability of the equipment, I thought about expressing the results as fold change (treatment/control) by setting the control as 1 (or 100%). But then, the control group would always be 1 (or 100%) and the SD would practically be 0.
I would appreciate any suggestions.
Thank you.
Dear Aristeidis E. Boukouris,
I suggest you to see links and attached files on topic.
https://www.bioconductor.org/packages/release/bioc/vignettes/DEP/inst/doc/DEP.html
https://www.nature.com/articles/s41598-019-49665-1
https://www.hindawi.com/journals/ijpro/2010/731582/
Article Detecting Significant Changes in Protein Abundance
Best regards
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