Hello Bioconductor forum,
I used Bioconductor package limma for analysis of differentially expressed genes in this Agilent microarray dataset available under https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=+GSE59408.
Now my question is: are there any alternative packages to limma for analysis of differentially expressed genes in microarray datasets? I would like to compare results for the differentially expressed genes I found with limma. I did some research but only found alternative packages to limma for RNA-seq data and not for microarray data.