How to handle and benefit from the spike-in controls in your arrays in R

Question

[Antonio R. Franco]

I have some Agilent one and two color arrays data that I have analyzed using the limma R package. I create the spottype.txt file that contains data including the spike-in used as internal controls. From the Agilent webpage, I can get information about their concentrations, etc

But I have found that the information to use these controls into your analysis is scarce, even if looking into the vignettes

Can you enlight me with some ideas, tutorials, etc on how to use these controls ?

Answer 1

[michael.ante]

Hi Antonio,

you can have a look at the ERCC-Dashboard (bioconductor and publication). Even if you didn't use the ERCC spike-in controls, you can feed the program with your own concentration table.

I used the ERCC-dashboard in terms of RNA-Seq control, but it also handles Microarray data.

Cheers,

Michael