Determining and separating Affy Chips from GEOquery?
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PyPer ▴ 20
@pyper-6819
Last seen 9.4 years ago
Australia

I am currently utilizing a dataset GSE14520 from the GEO website.

I understand that it utilizes two chips U133A and U133A 2.0.
For preliminary analysis I only need to utilize U133A.

Is there an easy way to sort the cel files into their appropriate platform? or do i have to write a script to do it?

geoquery affy • 749 views
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@james-w-macdonald-5106
Last seen 14 hours ago
United States

The two arrays were combined using matchprobes(), so in essence all you have are U133A arrays (the additional probesets that were on the U133A 2.0 array were discarded).

If you really care to only use the 133A arrays, you can use getGEOSuppFiles() to get the CEL files, then use read.celfile.header() in affyio, or readCelHeader() in affxparser to identify the array types.

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