[BioC] Zero variability in RMA

Angelo Canty canty at math.mcmaster.ca
Mon Jun 7 20:06:23 CEST 2004


I am analyzing a small microarray experiment with 5 RAE230_2 chips
with material from two strains of rat.

I loaded in the data using ReadAffy and then run the rma function to
normalize the data and produce the expression values.  In 486 (out of
31099) probesets, the expression values are identical over all 5
chips and in two others there was no variability within strain 
although there was across strains.  In either of these cases, I get
zero variability for the mean difference.  

I have examined the original probe level data as read from the CEL
files and there is variability across the chips in both the PM and
MM measurements so my conclusion is that this is an effect of the
rma or normalization steps.  Has anyone else witnessed this effect?
What is the preferred way to deal with this lack of variability?

Thanks for any help that you can provide.

|   Angelo J. Canty                Email: cantya at mcmaster.ca     |
|   Mathematics and Statistics     Phone: (905) 525-9140 x 27079 |
|   McMaster University            Fax  : (905) 522-0935         |
|   1280 Main St. W.                                             |
|   Hamilton ON L8S 4K1                                          |

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