[BioC] (no subject)

James MacDonald jmacdon at med.umich.edu
Wed Jun 29 04:06:50 CEST 2005

Hi Ariful,

Are these recent generation chips (hgu133plus2 or rat2302 or mouse4302)?
With these chips there is usually a pronounced dark band across the
middle of the image. I don't know if it is simply a moire pattern of
some kind or actually because those probes are hybridizing less, but I
almost always see this. As for the bright areas, are they directly in
the middle of the chip, with possibly another bright area in the upper
left corner? If so, these are different control probes, some of which
should be nearly saturated.

As long as the things you see are consistent from chip to chip, you are
probably OK. Problems usually arise when you have e.g., a much brighter
chip, or a big white blotch in the middle of a chip, etc.

And yes, you can background correct separately. See ?bg.correct

You might also try help.start() and peruse the help files for the affy
package. This is a great place to start.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
>>> "Islam, Ariful" <aislam at mail.smu.edu> 06/27/05 3:54 PM >>>
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




Department of Statistical Science

Southern methodist University

Dallas, TX

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