Standard error - clarification

[Arielb]

Dear MSstats team,

I am looking into some older result files (from version 3.3.4), and have a questions about the column SE. My understanding was that this represents the standard error of the effect size (the log2FC). However, when i sorted the table, the SE is the same for every protein across all the comparisons made (say i had ten comparisons in my matrix, i get ten different log2FC, but the same SE for each). I m not sure whether i mis-understand something or whether it was a bug. Maybe you could clarify ? either way, could you also suggest the clearest way to describe it ina figure legend ?

thanks, Ariel

[Meena Choi]

Error term is calculated by protein. If there are the same number of replicate per condition, SE is the same by protein.

Hope to help.

- Meena

[Arielb]

Hi Meena, 

Thanks for the clarification . This helps. So what would be the correct way to present the error term ? as error bars on each fold change ? or perhaps present it once per each protein ?

Thanks, Ariel

[Meena Choi]

error bas on each fold change. If there are different number of replicate per condition, SE will be different in a protein.