annotation of agillent array G3 Human Gene Expression v3 8x50
Entering edit mode
Last seen 4.8 years ago

Dear all,

I need to annotate data from agilent array. I use limma for differential expression. Which library caan I use for annotate genes.


microarray annotation agilent • 1.0k views
Entering edit mode
Last seen 16 hours ago
United States

If you read the data in using limma, you already get some annotation. As an example, using GSE86970:

> dat <- read.maimages(fls, "agilent.median", green.only = TRUE)
Read GSM2311277_V7T.txt
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Read GSM2311284_V20T.txt
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Read GSM2311286_V24T.txt
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> head(dat$genes[dat$genes$ControlType == 0,])
  Row Col ControlType     ProbeName  SystematicName
4   1   4           0  A_23_P117082       NM_015987
5   1   5           0 A_33_P3246448       NM_080671
6   1   6           0 A_33_P3318220       NM_178466
7   1   7           0 A_33_P3236322        AK128005
8   1   8           0 A_33_P3319925 ENST00000449753
9   1   9           0 A_21_P0000509       NR_024244

The SystematicName is now a mixture of RefSeq and GenBank IDs, Ensembl transcript IDs, which would be a bit of a drag to annotate. Luckily others have already done that for you. We can get the GPL for this array from GEO as well.

> z <- getGEO("GPL21061")
> zz <- Table(z)
> dat$genes <- cbind(dat$genes, zz[match(dat$genes$ProbeName, zz$ID),1:4])

Then you can do all the pre-processing and QC and comparisons, and when you use topTable, you will get all the annotations. Prior to doing topTable you might want to subset to just the columns of interest in the genes list item, as things like the Row or Col, etc are not usually of interest.


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