I am making a heatmap using RNA-Seq data in R. The heatmap shows gene expression values (RPKM) in different brain regions. I have the following code:
library(tidyverse) library(pheatmap) library(matrixStats) read_csv("prenatal_heatmap_data.csv") -> all_data all_data %>% column_to_rownames("Brain Region") -> heatmap_data heatmap_data %>% pheatmap()
Which generates the following heatmap:
I want to do a log2 transformation of the RPKM values so that I can do the Z-score standardisation of the data. I have log2-transformed the values using the following code:
heatmap_data %>% log2() -> heatmap_data_log2 heatmap_data_log2 %>% pheatmap()
However, when I try to create a heatmap using the log2-transformed values I get the following error:
I have looked at the log2-transformed data and I know that the reason I am getting this error is because in the original dataset, some of the RPKM values were 0. When these 0 values get log-transformed they become -Inf:
^ Original Data
^ log2 transformed data
I am not sure how to overcome this issue. I was wondering if it is necessary to do the log2 transformation of the RPKM values before doing the Z-score standardisation? I have seen that it is conventional to do the log2-transformation of the data.
Any advice is appreciated.