Bright spot on affymetrix chips

Question

[oganm]

I am doing some quality control on a bunch of affymetrix chip and I noticed a consecutively bright spot in every single one of these chips. I assume this has a technical use since I observed this in different chips. Can anyone tell me what it is? The image below is an example with exceptionally low overall intensity but that spot in the middle is shiny as always. Thus particular chip is Affymetrix U133 Plus 2.0. The image is generated by image() function of R on the affy object.

[GouthamAtla]

Its good to contact Affymetrix tech support for such questions.

Answer 1

[Dan D]

That's the control probe set. You should see that on every chip, so it's useful as a QC indicator.