Pre-processing for Agilent microarray data?

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19 months ago

survive • 0

Hi, is there any recommended pre-processing for Agilent microarray data?

I know there're frma and rma for Affymetrix microarray data, but I am not sure about Agilent.

I found a R package called AgiMicroRna but it seems to focus on processing data for analysis with the limma package.

Thank you.

affymetrix microarray gene agilent rna • 1.3k views

ADD COMMENT • link updated 13 months ago by 1769mkc ★ 1.2k • written 19 months ago by survive • 0

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I think limma does pretty good : http://bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf

ADD REPLY • link 19 months ago by Basti ★ 2.0k

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Hi, thank you for the reply. Since I'm not familiar with Agilent data, what are the standard way of pre-processing the data? For example, should I be doing background correction?

ADD REPLY • link 19 months ago by survive • 0

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That is covered in the linked document when searching "Agilent".

ADD REPLY • link 19 months ago by ATpoint 86k

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thank you!

ADD REPLY • link 19 months ago by solarchan7 • 0

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I was also looking for this. So we donot necessarily need the agilient R package to process the data?

ADD REPLY • link 13 months ago by 1769mkc ★ 1.2k

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