












•

RPM (Reads Per Million)
is a straightforward normalization method for Count data. It divides the raw read count by the total reads or the total mapped reads, and multiplies the result by 1,000,000.



•

Upper Quartile Scaling
applies a scaling
factor
based on upper quartile to scale each column. The within column upper quartile is calculated by excluding the rows of all 0 (or
missing
) values. Each upper quartile is further standardized by dividing by the geometric mean among all upper quartiles across columns to be the upper quartile scaling factors.



•

TMM (Trimmed Mean of
M
component) is a scaling normalization method for RNASeq data. The
M
and
A
components between the targeting sample (under normalization) and the reference sample are calculated for selecting partial data to take the weighted trimmed mean of the
M
component as the scaling factor corresponding to the targeting sample.



•

KMM (Kernel Density Mean of
M
component) is similar to TMM. The
M
and
A
components between the targeting sample (under normalization) and the reference sample are calculated for estimating the twodimensional Kernel Density and applying the density for the weighted mean of the
M
component as the scaling factor corresponding to the targeting sample.





