R with these packages installed: affy, limma, sva, org.Hs.eg.db, ggplot2

And you are supposed to need a cdf R package:
You can download from here.

Here are two example:
hgu133plus2hsrefseqcdf
hgu133a2hsrefseqcdf

This is the command line that to excute this script:

Rscript affy_limma.R data_path design_matrix_path result_path cdf_name 1 0.05

Only affy_limma.R is available now.

The first argument is the data files path, the second is the design matrix path.

The design matrix should include two columns and delaminated by tab. The first column is GSM IDs of RNAseq samples. The second column is the design of experiment. Usually control group shoud be upper and treatment group should be at the bottom. For example:

GSM10001	Control
GSM10002	Control
GSM10003	Treatment
GSM10004	Treatment

The third argument is the results path or output path, and is supposed to be a folder.

The fourth is affy chip's CDF package name. For example, you are suppose to set this argument like hgu133plus2hsrefseqcdf if you downloaded a package like hgu133a2hsrefseqcdf_22.0.0.tar.gz.

The fifth is fold change and the sixth is adjust P value.