I want to merging multiple GSEs with different GPLs(with R) ,but I don't know which package is suitable for merging, for this purpose, VirtualArray and InSilicoMerging packages do not efficient.
Could you explain what are you trying to do? GPLs describe different GEO platform (Sequencing, array or even RT-PCR) and unless they are measuring similar things, you can not merge them. On the top of that, you need to care about different normalization and overall normalization of merged samples.
I want to find similar genes between different GPL then compare expression level of these genes to find out which have significant difference.