Dear guys,
Do you have any experience when using limma for one batch of proteomics data, the log2FC is surprisingly high (1500-3000), but when checking the expression matrix, the value among the samples are pretty similar.
The design is ~0+ treatment, which seems quite normal, any possible reasons? It does work well for other data, quite strange...
Many thanks!
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alwayshope •
It's a sure sign the data has been input to limma incorrectly.
Thanks a lot! Turns out the input matrix has not been normalized...
Thank you all very much!
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You will need to show data, code and some plots to illustrate.