I got data from Agilent microarrays that I have successfully analyzed myself with limma once the company have sent me all the data. But this company has not sent me the SpotType.txt file that will allow me to represent the spike-in controls in the plotMA figures. I've been looking through Internet the way of creating this file, to figure out its structure and content, and I have some doubts.
I have not problems in identifying the rows containing the regular controls (DarkCorner, GE_BrightCorner...) and the spike-in controls as well from the data$genes$ControlType (looking for those that are not 0)
I believe that I need to include the SpotType, Name, ID, col, and cex of each of the probes, but I will appreciate a lot if somebody can give further information or clues about what should I use to generate this file. In particular, I have doubts about what to use as SpotType, Name and ID from the EListRaw data
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Antonio R. Franco
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I think a header of such a file can help me..