You need to be clear about who did what. At the moment this reads as though you did it. Did you grow the plants and run the arrays or did someone else? If you did this stuff then the methods for this needs to be MUCH more detailed.
You need analysis scripts and package versions.
You need to justify the use of PUMA over limma. Why do you believe that there is a genreal shift in expression?
Label your template and coding strands on figures.
Read through of Chapter 5.
Couple of things here:
You need to be clear about who did what. At the moment this reads as though you did it. Did you grow the plants and run the arrays or did someone else? If you did this stuff then the methods for this needs to be MUCH more detailed.
You need analysis scripts and package versions.
You need to justify the use of PUMA over limma. Why do you believe that there is a genreal shift in expression?
Label your template and coding strands on figures.
I think you need p-values on some of your claims.