I'm a beginner at processing microarray data. I have 114 CEL files (chip: GeneChip™ miRNA 4.0 Array). I tried the following 2 ways to get the signal values and the output is different with no consistent direction.

1.Transcriptome Analysis Console 4.0

 (1) Analysis Type: Expression(Gene) 
 (2) Summarization: RMA+DABG(detection above background)

2.rma() function from the Oligo package in R Bioconductor

I tried to tune the parameter in DABG but the signal values are still the same when using TAC. So I'm confused why the signal values from 2 software are different?

Here is part of my data from 2 software(Left: TAC/ Right: R).