Question

Hello All can any one please help?

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sumode • 0

@sumode-20295

Last seen 5.1 years ago

how to custom select cel files from GEO data sets? I selected a few from 115 samples but the GEOquery package extracts all.

microarray bioconductor R • 335 views

ADD COMMENT • link 5.0 years ago sumode • 0

score 1 · Answer 1 · 2019-04-27

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 23 minutes ago

United States

In your sapply call, you don't specify where to put the decompressed files. But you don't need to do that step anyway, as both affy and oligo can work with gz files anyway

ADD COMMENT • link 5.0 years ago James W. MacDonald 65k

score 0 · Answer 2 · 2019-04-27

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sumode • 0

@sumode-20295

Last seen 5.1 years ago

thank you. but the issue i see is different. i am unable to understand how i can use custom (.CEL)files that i downloaded from GEO. What should I do?

ADD COMMENT • link 5.0 years ago sumode • 0

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If you go back and edit your original question like that, then obviously my answer will no longer apply. And you should also note that your edited question isn't sent out as an email, so nobody will notice unless they come to the support site directly.

Put a different way, don't do that.

Your original question was about some hgu133plus2 arrays, which are not custom, and your edited question asks about getting a subset of the arrays, and your answer (which unless you are actually answering something you shouldn't use the answer question box) asks about custom arrays.

We aren't mind readers here, so perhaps you have a single coherent question to ask?

ADD REPLY • link 5.0 years ago James W. MacDonald 65k