Interreplicate statistics for microarray data?

Question

[hakimelakhrass]

Hello!

I have an experiment with 5 timepoints and 9 replicates per time point. This is .CEL data from hugene 2.0 arrays. Does any one have any idea how to look at the statistics between the replicates at each time point? I am trying to identify and issue that might effect the total analysis.

Thank you

Answer 1

[Amitm]

hi, this BioC pkg, snm, allows you to add covariates like (date of scan, age, etc.) in addition to inter-replicate normalization. Post-normalization, you get a couple of diagnostic plots like p-value distrib. and intensity-dependent effects. See the manual for more details