I am having trouble with an Agilent miRNA micro array experiment:
I have mouse samples tested using Agilent.miRNA.21828_v15_0 G4472B and human samples tested using Agilent.miRNA.21827_v12_0 G4470C. Both chips are rather old designs from 2007-2008.
What my problem is that only about 30% of the measurements provide a detectable value. The rest seems to be not detected. We have done other miRNA arrays using other platforms that show around 50%+ measurements. (the chip designs are comparable) All quality control indicators provided by the platform are either excellent or good. (nothing to evaluate)
The array facility that did the work assured me that 20-30% detected calls are the norm for them when using Agilent chips.
I honestly am surprised by this. As it happens Agilent had a seminar at our university and I asked the Agilent representative and he was shocked/surprised/puzzled by 20-30% detected calls. Another research group that uses the Agilent chips for years was similarly surprised with our results and suggested that they typically detect >50% of the probes.
Pew... to finally get to my question: How many informative calls do you get on Agilent miRNA arrays?
(side note: I tried excluding experimental bias by ignoring the experimental conditions and only focusing on the control samples. The experimental conditions behave similar to the control samples though)
We too had low calls using 029297 design...