Using Bioconductor To Analyse Beadarray Data: Difference between revisions
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**beadarray | **beadarray | ||
**limma | **limma | ||
**annotation data for the array (normally illuminaMousev2BeadID.db) | |||
<pre> | <pre> | ||
source("http://www.bioconductor.org/biocLite.R") | source("http://www.bioconductor.org/biocLite.R") | ||
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==Annotation of Expression Sets and Fitted Data== | ==Annotation of Expression Sets and Fitted Data== | ||
*To see all possible annotation criteria use: | |||
<pre> | |||
library(illuminaMousev2BeadID.db) | |||
illuminaMousev2BeadID() | |||
</pre> | |||
*Normally you want to annotate with at least the gene symbol and gene name. Add other criteria as required | |||
<pre> | |||
ids = rownames(exprs(BSData)) | |||
GeneName = mget(ids, illuminaMousev2BeadIDGENENAME, ifnotfound = NA) | |||
symbol = mget(ids, illuminaMousev2BeadIDSYMBOL, ifnotfound = NA) | |||
anno = cbind(GeneSymbol = as.character(symbol), GeneName = as.character(GeneName)) | |||
</pre> | |||