Question: Pooling microarray data
0
gravatar for grayapply2009
2.7 years ago by
grayapply2009170
United States
grayapply2009170 wrote:

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?

microarray pool • 803 views
ADD COMMENTlink modified 2.7 years ago by Jean-Karim Heriche18k • written 2.7 years ago by grayapply2009170
2
gravatar for Jean-Karim Heriche
2.7 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

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.

ADD COMMENTlink written 2.7 years ago by Jean-Karim Heriche18k

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

ADD REPLYlink written 2.7 years ago by grayapply2009170

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.

ADD REPLYlink written 2.7 years ago by Jean-Karim Heriche18k

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.

ADD REPLYlink written 2.7 years ago by grayapply2009170
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