PCA plot

[gsk7757]

Hello everyone,
I tried to run RScript code/create_pca.r to create a PCA plot. However, the code returns the below error.
Error: Counts file, Design file and the number of samples must be specified at the commandline
Execution halted

I have mentioned counts, design, and number of samples in the command line. Here is how I have mentioned

How to run?

Rscript summary_plots.r <counts_file> <design_file> <number_of_samples>

Example: Rscript summary_plots.r counts.txt design.txt 6

Design file example:

Sample Condition

C1dedup control

C2dedup control

C3dedup control

E1dedup experiment

E2dedup experiment

E3dedup experiment

Please help.

[ialbert]

I would recommend following the workflows in the Biostar Workflows

https://www.biostarhandbook.com/books/workflows/

there is an entire section of RNA-Seq methods

All the analysis code has been rewritten in a more elegant and robust manner.

The "RNA-Seq by Example" book will be soon (within weeks) be rewritten to use the same codebase as the Workflows book.

[gsk7757]

Thank you. I will follow the workflow then. I was actually following the book RNA-seq by Example.