I'm going to draw a heatmap for DE analysis. According to my research, these are the steps:
1- I sorted genes by their FDR and chose 30 of the most significant genes.
2- I'm using the normalized read counts of the chosen genes to draw heatmaps.
3- When I'm going to scale my normalized read counts using package "Pheatmap", I choose "scale by row". (Rows are genes)
Now my problem is this package scales the data to mean 0 and standard deviation 3. While I'm gonna scale them to mean 0 and SD 1.
Would you please help me know what I can do? can "pheatmap" scale my data the way I want?