How to know if it is 'one-color' or 'two-color' microarray?
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7.6 years ago

Hello,

I would like to know how to check if the studied microarray (such as GSE13105 from GEO) is one-color or two-color array?

For example, I can obtain the raw data (e.g., A.CEL), if there is a way to know the A.CEL is one-color or two-color microarray? or If I know the microarray platform (such as GPL4372 in NCBI GEO), how can I know this platform is one-color or two-color microarray or others?

Thanks,

Kevin

microarray RNA-Seq ChIP-Seq sequencing • 5.5k views
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Research. Look up the GPL4372. It will have a name and a manufacturer and a brochure. Maybe even user manuals.

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The pData should indicate whether there is something on channel two (if one exists): have a look at characteristics_ch2.X

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thanks for your reply.

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May I ask, for the example shown (GPL4372), where specifically did you find the pData/characteristics_ch2.X. I've just asked a similar question here: How to identify whether a microarray data set is single channel intensity?

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The one-colour vs two-colour thing is an experiment-specific choice. You could use an Agilent array for either one- or two-colour experiments, for example. So you actually have to look at the GSE, rather than the GPL information to determine whether a given expt was 2-colour.

gse <- getGEO('GSE13105')
pData(gse[[1]]) # contains annotations for both ch1 and ch2
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