Hi all.
I am doing analysis using microarray data and want to use LIMMA to differentially express. Do you know if LIMMA Voom is ok for that as as far as I know it is better for RNA Seq and LIMMA trend is better for Microarray but I would much rather use LIMMA Voom if that is possible at all. Let me know what you think as as far as I know LIMMA was originallly developed for Microarray?
Dear @Jonathan,
Yes, limma voom is good for microarray data. A colleague of mine worked with that some years ago to predict differentially expressed genes and it was one of the best methods, at that time. I point out at that time. I have not worked with microarray data for a while and I am not sure of the state-of-the-art methods, but here is a selection of literature about limma-voom for microarray data.
https://ucdavis-bioinformatics-training.github.io/2018-June-RNA-Seq-Workshop/thursday/DE.html
I hope that is of some help.
Have a good week and best wishes,
Florian