[BioC] 2 color data...

James W. MacDonald jmacdon at med.umich.edu
Wed Jul 19 15:37:23 CEST 2006

Hi Miles,

milesg at bu.edu wrote:
> HI, my name is Gregory Miles. I'm at Boston University and was given this 
> address by Dr. Carey (I went to a seminar of his last week) at the Harvard 
> medical school and was told that I could ask my question about 2 color data to 
> you. On the mouse microarray dataset we have, there are two colors, and 
> therefore two values that can be below background. When both values are above 
> background (zero_barcode on our chip), we keep the data and when both are 
> below we eliminate the data (they become NA). I imagine this is a correct 
> approach, but what should be done regarding the data that has one intensity 
> below background and one above. Would it be best to keep the good value? Do we 
> eliminate the entire gene from entry into bioconductor? Perhaps there is a way 
> to specify to bioconductor that this is the case (by entering a background 
> value) and allowing it to handle the data abstractly? Or is it best to let 
> Bioconductor look at them as NA's. Any help would be greatly appreciated. 

Probably the easiest way to handle such things is to use the limma 
package and when you do background correction, use the 'normexp' method, 
which ensures that none of the background corrected values will be below 

This is probably not critical for those genes that are both below zero 
(since you probably want to ignore those anyway), but you certainly 
wouldn't want to ignore a gene where one sample is below zero and the 
other is (possibly) a large value.

If you want to use limma, I would strongly suggest perusing the user's 
guide. The learning curve can be steep, especially if you don't have a 
statistical background (load limma, then type limmaUsersGuide() at the R 



> Thanks!
> -Greg Miles
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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