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Microarray Suite Software (GeneChip® Analysis Suite)
The 3' to 5' ratio for one internal control looks fine, but the ratio for another internal control is high. Is my sample okay?
Your samples are probably fine. This is, most likely, a sample-related issue and not caused by sample preparation. The GeneChip® expression assay protocol does not preferentially amplify some transcripts over other transcripts. Every cRNA is transcribed from the same T7 promoter incorporated during the cDNA synthesis step with the dT T7 primer.