Will setting control spots to zero affect normalization within/among
arrays?

 

I've inherited a set of scripts for gene expression analysis of Agilent
two-color arrays.  We are using ScanExpress software by Perkins to get
convert the images to R,G intensities so "read.maimages" and readGAL
have been adapted.  

 

I just noticed that there is a line that sets the RG$genes$ControlType
values to zero if they are positive or negative controls.  Then those
are included in the weights file.

 

Is this a problem?  Should I be using something more like
wtIgnore.Filter?   

 

We have 1502 control spots / array.

 

Thanks,  

 

Kathryn Steiger

Illumigen Biosciences

Seattle, WA

 

 

 


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