Using Bioconductor To Analyse Beadarray Data: Difference between revisions
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[[Category: R]] | [[Category: R]] | ||
[[Category: Bioinformatics]] | [[Category: Bioinformatics]] | ||
[[Category: Bioconductor]] | |||
==Software Requirements== | ==Software Requirements== | ||
*R, get from | *R, get from [http://cran.r-project.org/ CRAN] | ||
*Bioconductor, get from | *Bioconductor, get from [http://www.bioconductor.org/download Bioconductor] | ||
*Bioconductor packages. Install as needed: | *Bioconductor packages. Install as needed: | ||
**beadarray | **beadarray | ||
**limma | **limma | ||
**annotation data for the array (normally illuminaMousev2BeadID.db) | **annotation data for the array (normally illuminaMousev2BeadID.db) | ||
*To install bioconductor packages use: | |||
<pre> | <pre> | ||
source("http://www.bioconductor.org/biocLite.R") | source("http://www.bioconductor.org/biocLite.R") | ||
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data = cbind(anno,data) | data = cbind(anno,data) | ||
write.csv = (data, file = "Filename.csv") | write.csv = (data, file = "Filename.csv") | ||
</pre> | |||
*Remember that the expression set is Log2 adjusted, so to look at absolute expression levels use 2^value. | *Remember that the expression set is Log2 adjusted, so to look at absolute expression levels use 2^value. | ||