Hi bioconductor users,
I am a PhD student working on stem cells from human umbilical cord blood. I
got data from our sorted cells relying on the HG-U219 platform from
Affymetrix. What I want to do is to compare our data to data from public
databases such as GeneExpressionOmnibus or ArrayExpress, but unfortunately
these data are all based on the HG-U133 platform.

So my question is: What would be the simplest approach to achieve this? What
would be the best approach to achieve this?

I'm thinking of 2 scenarios:
First scenario:
1. Get an expression table for both datasets (U219 and U133)
2. label both datasets with "comparable" identifiers, eg UniGene Id or
GeneBank A#
3. get new expression tables with only entries present in both datasets

Second scenario:
1. get raw data of both datasets
2. import CEL files from U219 and convert it to U133 format
3. combine both datasets into 1
4. do normalization of all data together

Please tell me it is possible, and if then how to do it. I'm pretty sure it
is possible, but I'm a R and BioC novice and don't know every
function/package.

Thanks in advance, Andreas

PS: Is it problematic that there are only perfect match probes on the
HG-U219 and no MMs?

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