[BioC] Minimum no. of chips for express/rma/gcrma etc

[James MacDonald]

I think you can argue that the batch methods (rma, gcrma) require more
than a certain number of chips to accurately estimate the parameters you
are modeling. However, this probably only applies to genes that are not
changing that much, so you will still see the ones that really change.

I don't think mas5 is affected by the number of chips.

Best,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> Aedin <aedin.culhane at ucd.ie> 03/15/04 07:20AM >>>
Dear BioC
Are rma/gcrma/mas5.0/ etc limited by a minimum number of chip (.cel)
files?

I am calling expression values on a dataset with only 2 chips
(treated/control, pooled RNA from n=5). Is 2 chips too few .cel files
for
these methods?

Thanks for your help
Aedin

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