OK, I can understand. so if the SIn values (displayed) are log transformed values. Can we take antilog of these values to come back to the actual fractional values.
Since, I want to compare two samples where i want to represent the difference in the quantity of each protein as fold change. Am I needed to do it separately in excel or other platform where i can calculate the ration using fractional (normalized SIn values) for each of the proteins. Thank you On Wednesday, August 16, 2023 at 1:37:05 PM UTC-7 [email protected] wrote: > Here's a detailed mathematical explanation of SIn: > https://doi.org/10.1038/nbt.1592 > > Briefly, the normalization process produces fractional representation of > quantities, i.e. 0.01, 0.052, etc. These are then log-transformed, which > results in values that typically range from -5 to -30, but are always > negative because they are log-transforms of values less than 1. > > These negative values can be adjusted by applying a scalar to the values > (such as +30) so that all values are greater than 0. Alternatively, there > is an option in StPeter (-s) where you can specify a total protein amount > loaded into the instrument and StPeter will scale all the quantities to > that amount. Note that this isn't an absolute value for each protein, > because StPeter is standardizing the results to the sum of all *observed > *proteins > (not the ones you didn't identify), but it still puts all values in an easy > to conceptualize, and positive, scale. > > These standardized numbers are comparable across samples (to obtain > ratios) so long as the samples were acquired with the same instrument > method and chromatography conditions. > > Cheers, > Mike > > On Wednesday, August 16, 2023 at 10:53:34 AM UTC-7 sudarshan kumar wrote: > >> and >> in StPeter what does negative SIn scor emean? I see all of them being >> negative >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/af5ca34a-32b9-476e-98cd-185c21b6c483n%40googlegroups.com.
