10.20387/BONARES-2657-1NP3
Beule, Lukas
Lukas
Beule
University of Goettingen
Scaling with ranked subsampling (SRS) algorithm for the normalization of species count data.
BonaRes Data Centre (Leibniz Centre for Agricultural Landscape Research (ZALF))
2020
Petr Karlovsky
University of Goettingen
2200-07-02
2020-07-01
2020-07-01
application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
text/comma-separated-values
File-Geodatabase (gdb)
An implementation of SRS in R is available for download: https://b-web.bonares.de/smartEditor/rest/upload/ID_7049_2020_05_13_SRS_function_v1_0_R.zip
Scaling with ranked subsampling (SRS) is an algorithm for the normalization of species count data in ecology. So far, SRS has successfully been applied to microbial community data.
SRS consists of two steps. In the first step, the counts for all OTUs (operational taxonomic untis) are divided by a scaling factor chosen in such a way that the sum of the scaled counts (Cscaled with integer or non-integer values) equals Cmin. In the second step, the non-integer count values are converted into integers by an algorithm that we dub ranked subsampling. The scaled count Cscaled for each OTU is split into the integer-part Cint by truncating the digits after the decimal separator (Cint = floor(Cscaled)) and the fractional part Cfrac (Cfrac = Cscaled - Cint). Since ΣCint ≤ Cmin, additional ∆C = Cmin - ΣCint counts have to be added to the library to reach the total count of Cmin. This is achieved as follows. OTUs are ranked in the descending order of their Cfrac values. Beginning with the OTU of the highest rank, single count per OTU is added to the normalized library until the total number of added counts reaches ∆C and the sum of all counts in the normalized library equals Cmin. When the lowest Cfrag involved in picking ∆C counts is shared by several OTUs, the OTUs used for adding a single count to the library are selected in the order of their Cint values. This selection minimizes the effect of normalization on the relative frequencies of OTUs. OTUs with identical Cfrag as well as Cint are sampled randomly without replacement.
5.81
15.77
47.26
54.76
Federal Ministry of Education and Research
031A562A
BonaRes, SIGNAL
Federal Ministry of Education and Research
031B0510A
BonaRes, SIGNAL