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How can I normalize datasets from [miRNA-1] Affymetrix Multispecies miRNA-1 Array and [miRNA-2] Affymetrix Multispecies miRNA-2 Array simultaneously?
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The short answer is that you can't. This is true of pretty much any microarray, not just these two. To normalize a set of arrays, they have to contain the same content, and these two arrays have different content, so normalizing together doesn't make sense.
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It depends. If you have analyzed the same sample types on each array, then you could normalize separately, subset to the overlapping probes and then analyze using a batch effect. An alternative would be to use meta-analysis instead, say with the GeneMeta package.
If however you have something like all the treated samples on one array and the controls on the other, then there is no way to distinguish technical differences (which will predominate) from real biological differences. If that is the case then the experiment is pretty much dead on arrival.
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Are you working with a data that uses miRNA-1 Affymetrix Multispecies miRNA array? I downloaded a dataset that used this array, but they don´t have any information about it at the Affymetrix website.