Hi all,

All my apologies for this trivial question, but I haven't been able to find a solution anywhere.

I've got a MAlist object encompassing the expression data of 62 arrays.

In the chapter 7 of the limma user guide it is advised to filter for probes that are not expressed, by keeping only probes expressed above a background threshold in an least some arrays.

It is is said to look for examples in case studies 15.3 or 15.4, but certainly due to the evolution of the user guide those chapter are not case studies anymore. I've looked into the case studies of later chapters and unfortunately haven't found an example of filtering MAlist based on expression.

If anyone have any advices on how to determine a background threshold, and how to filter a multi-arrays MAlist object for low expressed probes it would be very helpful to me.

Thank you for your help

Filtering is more important for single channel platforms. With two color arrays, normexp background correction and trended eBayes, you can skip the filtering step.

Of course, special control probes, like the bright corners on an Agilent array, should still be removed.