Question: BioMart Attributes/Filters missing
0
gravatar for terka
3.8 years ago by
terka0
European Union
terka0 wrote:

Hi, 

I would like to use getBM function to get ENSEMBL gene identifiers to ProbeNames from Agilent Whole Mouse Genome Microarray Kit (design ID 014868), 4x44k. However, in the available filters, I can only find Agilent WholeGenome 4x44k v1 probe ID(s) and Agilent WholeGenome 4x44k v2 probe ID(s). Do you have any suggestions about how can I find the IDs to the specific microarray that I used?

 

Thanks a lot in advance, 

 

Teresa

ADD COMMENTlink modified 3.8 years ago by James W. MacDonald51k • written 3.8 years ago by terka0
Answer: BioMart Attributes/Filters missing
1
gravatar for James W. MacDonald
3.8 years ago by
United States
James W. MacDonald51k wrote:

There are at least two other ways you could approach this. First, if you are using limma to do the analysis (and you probably should be doing that), then when you read the data into an RGList, the 'genes' list item will contain accession numbers that you can use to map to Ensembl using the org.Mm.eg.db package. Something like

library(limma)
library(org.Mm.eg.db)
dat <- read.maimages(<filenames go here>, source = "agilent.median")
gns <- dat$genes

## there should be a column called 'Systematic name' or something like that, which contains the accession numbers. You can then map using mapIds():

ensgene <- mapIds(org.Mm.eg.db, as.character(gns[,<correct column number goes here>]), "ENSEMBL","ACCNUM")

An alternative would be to get the data from GEO. You could use GEOquery to get those data, or just download by hand and parse out the column containing the Ensembl IDs.

ADD COMMENTlink written 3.8 years ago by James W. MacDonald51k

Great, this helps a lot! Using mapIds did it really well. Thank you, James!

ADD REPLYlink written 3.8 years ago by terka0
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