可以看出来clr函数是根据每行(这里即每个样本)来计算的g(x)。 因此,在使用clr函数时一定要确保taxa在行,样本编号在列。或者可以配合apply函数使用 apply_clr2.png 另外一个问题是这里建立的OTU丰度表没有0值,但在实际的数据中,经常会存在许多的0值,显然不能直接用clr进行数据的转换。 但是我在使用clr函数进行转...
在分析肠道微生物数据中，一般会对数据进行一定的转换，以使数据尽可能的服从正态分布。常用的方法有 Centered Log-ratio (CLR) transformation和 Cumulative Sum Scale (CSS) transformation等。这里介绍一下在R中如何进行CLR转换。 CLR 转换的公式如下：明白clr的基本原理，在R中的实现相对...
Centerd log-ratio (clr) transformation and robust principal component analysis of long-term NDVI data reveal vegetation activity linked to climate processes. Climate 2015; 3: 135-49.Faith, M. Centered Log-Ratio (clr) Transformation and Robust Principal Component Analysis of Long-Term NDVI Data ...
This study uses a centered log-ratio (clr) transformation approach and robust principal component analysis (PCA), on a long-term Normalized Difference Vegetation Index (NDVI) dataset to test its applicability in analyzing large multi-temporal data, and potential to recognize important trends and ...
Identification of helminth associated OTUs by centered log-ratio (clr) transformations and sparse Partial Least Squares Discriminant Analysis (sPLS-DA).Soo, Ching LeeMei, San TangYvonne, A. L. LimSeow, Huey ChoyZachary, D. KurtzLaura...
In addition, using data visualizations, I will highlight some details about the centered log-ratio (CLR) normalization of antibody-derived tag (ADT) counts that may be overlooked. In this method chapter, I provide detailed steps to generate CLR-normalized CITE-seq data using cloud computing ...
Centered log ratio transformationJames M. Curran