How To Download Dataset For The Microarray Data Analysis From Ncbi For Affymetrix ?

Hello,

How to download affymetrix microarray data (cancer data compared with normal data should contain maximum of 4 samples) from the ncbi? And how the data input file should be? I'm using R program limma package in windows for the analysis purpose. Please help.

ncbi microarray limma affymetrix

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updated 3.4 years ago by Ram

• written 12.9 years ago by Arpitha Hebbar

1 answer

The GEOquery bioconductor package is specifically designed to solve this problem:

http://www.bioconductor.org/packages/release/bioc/html/GEOquery.html

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written 12.9 years ago by Sean Davis

cant i use limma package for GEO datasets ?

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written 12.9 years ago by Arpitha Hebbar

Of course. GEOquery simply gets the data into R. Once the data are in R, you can use any R-based workflow or tool that you like.

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written 12.9 years ago by Sean Davis

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