Dear list,

I would like to have your opinions on the following subject.

In hospital-studies most of the time we get more than 200 arrays per
study.It is evident that the arrays have significant differences among them
due to different array batch and many other conditions ie technical
competence, hybridization difference due to time span , circadian rhythm ,
fresh sample or not->different time from RNA extraction to hybridization ,
and others. How can we cope with the many uncontrollable factors and be able
to use 80 , 200 or even a higher number of arrays at the same analysis
fixing for any of the uncontrollable effects.

I am using mostly Affymetrix arrays , Hu133plus2 , MOE Gene 1 St , Moe 430 2
, and currently my favorite software apart from Bioconductor are Partek's
Gene Suite (which -at least according to the manual- can fix for
uncontrolled effects) , and Genespring due to the magnificent cluster
algorithm that incorporates.

Thanks in advance.

T. Paparountas
www.bioinformatics.gr

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