I am running a DE analysis with limma using a one-color microarray, and got the toptables indicating those genes which are differentially expressed.
My colleague (and also myself) want to know, however ,the level of gene expression between individual contrasts for each of the genes that give rise to the LogFoldChange value
We need to know whether a DE gene changes from a low, medium or high expression in the control to a lower or even a higher expression in the other condition included in the contrast
To my understanding, AveExp gives the log2 Expression mean level of each of the gene in all the compared arrays.
Is there at least a way to know the normalized level of expression of the control array in each of the genes of the array ?.