[BioC] (no subject)

[Islam, Ariful]

I am a graduate student and new in the field of microarray data analysis. I am learning how to handle affymatrix's genechip arrays. In my data set there are 16 arrays. Image plot shows a dark horizontal area in the middle of the images. There are also two little bright areas in the images of all the arrays. The dark horizontal strip and the spots are in about the same position of the images (probe level data). What needs to be done to correct these(If at all)? Could  anybody please mention some relevant references. Can I also background correct the probe level data independently (not within RMA)? I will appreciate your response.

Thanks.

 

Ariful

Department of Statistical Science

Southern methodist University

Dallas, TX