[BioC] Two rma questions

James MacDonald jmacdon at med.umich.edu
Thu Apr 15 17:15:20 CEST 2004

Ah. In this case, since the two strains may be quite different, it may
be better to normalize separately. 


James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> Simon Kidd <kidd at mail.rockefeller.edu> 04/15/04 10:42AM >>>
At 8.50am -0400 15/4/04, James MacDonald wrote:
>For your first question, it is almost always preferable to run rma on
>all samples in a set together rather than in two batches. For the
>question, the bug only concerns justRMA and justGCRMA, so rma and
>are not affected.

Thanks, however my collaborator thinks I did not phrase my question 
very well and did not emphasis enough that the genetic background of 
the strains could be very different, so this is what she thinks the 
question should be:

>We have performed two experiments. One compares fly strain A with 
>mutation M to fly strain A with a duplication for the wild type gene 
>M. The second experiment compares fly strain B with the same 
>mutation M with a different duplication for the wild type gene M. 
>Aside from the particular mutation we are assaying the genetic 
>background of the strains could be very different.  If one 
>normalizes  arrays from different tissues using dChip, it is 
>suggested that the arrays get normalized separately. Is this also 
>true for RMA or should they be normalized together?

If the strains are very different should they still be normalised

Thanks again.


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