How To Combine Two Types Of Affymetrix Genechip Results?

Question

[Gangcai]

Dear All, I have two sets of Affymetrix GeneChip data, one from GeneChip® HT MG-430 PM Array Plate and another from GeneChip® Mouse Genome 430 2.0 Array. According to official description, they use the same kind of technology, however they have different probset ids and different probe-sequences. My question is how can I combine those two datasets for comparison?

Thanks in advance.

[boczniak767]

Gangcai, you can join your data as shigeta wrote and try metaanalytic approach, i.e. something to transform data from different experiments to the same scale. Take a look at metaArray, GeneMeta, RankProd, metahdep packages. [?]Somewhere in these tutorials is example of joint analysis of several Affymetrix experiments.[?] HTH

[Shigeta]

This can be done by taking your log2 difference results from the 2 separate arrays and taking the identical probe set names and comparing them. The two have almost the same probe set contents. Any differences, if any, are not likely to be of biological consequences.

As with other microarray data, scaling data from different experimental runs can be done (esp in this case as they are essentially the same array), but often don't get the best results because of variance between samples, prep, hybridization conditions, etc.

[Gangcai]

Hi shigeta, thanks for your reply. I have checked the probeset names, and only 64 probes have exact same ids between those two GeneChips.

[Shigeta]

there is a resource on affymetrix.com called a comparison spreadsheet. they should be available for these 2 arrays - they are less exact unfortunately as the probes are not identical.