I am trying to work with limma from Bioconductor to calculate the p-values and foldchange values and find differentially expressed genes.
My data looks like this.
1. CYTO Value
ABC1 2.3
ABC2 2.3
ABC3 2.5
...
PQR1 3.1
PQR2 3.2
PQR3 3.1
I want to use the limma package to first compute design = model.matrix(~0+group) and then fit <- lmFit(Data$VALUE , design) after which I can use the eBayes() function and calculate p-values and fold change values.
NOTE: We are trying to find which gene EG: ABC1, is more differentially expressed then another.
2: gene name is a combination gene_name and visit info eg: ABC1 (1 is the 1st visit)