My question is about handling a GEO SOFT file from a "dual channel" microarray. I need to summarize and extract a probe set and genes with significant and high FC, like the topTable function of limma. I'm familiar with GEOquery, and it's perfect for downloading and converting GDS,GSE to ExpressionSet (readable by limma) via GDS2eSet. But GEOquery has a limited function and in many cases encounters error. Manipulation by spreadsheet software is not my desired.