Pooling microarray data

Question

[grayapply2009]

I am doing a metadata study. In this study, I need to pool all microarray datasets of mouse gonad. But I found these datasets were generated with different platforms. Is there a way that I can annotate these probes from pooled data?

Answer 1

[Jean-Karim Heriche]

You need to map all probe sequences to the same annotated reference genome. You might also be interested in this paper about meta-analysis of microarray data.

[grayapply2009]

Thank you, my friend. So there is no easy way to map probes across multiple platforms if i don't have the probe sequences?

[Jean-Karim Heriche]

If you're lucky, the manufacturers may have released their probe sequences and Ensembl may have already mapped them. See here and this example script.
As a less clean alternative, you could try mapping gene IDs from the different experiments/platforms to the same reference.

[grayapply2009]

Looks like a lot of trouble. I'll just merge the arrays done on the same platform I can find. Thank you very much, Jean.