I need to analyse differential gene expression from a set of microarray data using ballgown software. Please guide me how can i load my data in ballgown software? I have already used ballgown for differential gene expression of rna sequencing data?
Not too much help about R-based software from this side. If you want something easy to analyze your microarray data, give a try to AltAnalyze (http://altanalyze.org/). It works on Windoze and Linux and uses pretty much the same algorithms as R for normalization and differential expression.
Microarray and RNA-seq are different technologies and care should be exercised if you want to use algorithms designed for one technology on another. I would recommend you to use microarray specific tools instead.