After posting my first email, I realized that rma and gcrma does the normailization on probe level and across all the arrays in the group. But SNOMAD seems working on pair chip comparison only (probe level? not sure, the third normalization of SNOMAD should be at probe level instead of probe set) I wonder if after the rma I can input the data to SNOMAD to do the mean normalization and variance correction on intensities at the probe set level. Thanks. Lizhe -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 2619 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040319/8ca224e4/attachment.bin

you sure can. but turn off the normalization and background correction on snomad. the normalization because you already normalized and the background correction beacuse affy expression measures dont have locations (they are averages of probe intensitites from various locations) On Fri, 19 Mar 2004, Lizhe Xu wrote: > After posting my first email, I realized that rma and gcrma does the normailization on probe level and across all the arrays in the group. But SNOMAD seems working on pair chip comparison only (probe level? not sure, the third normalization of SNOMAD should be at probe level instead of probe set) > > I wonder if after the rma I can input the data to SNOMAD to do the mean normalization and variance correction on intensities at the probe set level. Thanks. > > > Lizhe >