DESeq2 input for pydeepinsight #60
Description
Hello, and thank you for developing this amazing package.
I am a data science student currently working with human bulk RNA-seq data, and I am using your tool to convert these data into image representations.
I would like to ask for your recommendation regarding the most appropriate input format. Specifically, would you advise using:
- raw count data
- data transformed using the variance stabilizing transformation (VST) from DESeq2
In addition, depending on the chosen input, if I understand the documentation correctly, you recommend applying an additional transformation. In this context, would the most suitable approach be to directly apply min–max scaling to my data, or to use the norm2scaler method that you developed and describe in your documentation?
Thank you in advance for your guidance.