How to create an AffyBatch object using a data matrix?
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4.6 years ago
komal.rathi ★ 3.9k

Hi everyone,

I have previously created an ExpressionSet object using a data matrix as input like this:

ExpressionSet(assayData = dat)

Then I usually use phenoData and featureData to set the sample and gene level annotation.

I wanted to know if it is possible to create an AffyBatch object in a similar manner?

Thanks!

affy affyBatch matrix • 2.4k views
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4.6 years ago

Could you explain better what are you trying to achieve? AffyBatch extends eSet, but it is really particularly used for batch-affymetrix data, so that the annotation etc come from affy CDF-files. And its particular structure is such that all the affy-related information are stored (pm, mm, probes, etc) insdie it. So unless you start from affy-CELL files, I am not seeing a particular need for AffyBatch objects (and it might not be possible also). I'm guessing that you have a data-matrix and you would like to use some functions from affy-batch processing protocol. In that case, check that the function that you need might work directly on eSet (rather than AffyBatch)

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Thanks - I will create an eSet instead. If you move your comment to an answer, I will be happy to accept it.

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the comment moved to answer now

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