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Old 04-11-2011, 01:07 AM   #1
Azazel
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Location: Japan

Join Date: Oct 2010
Posts: 52
Default Comparing detected genes. Coords for probesets of Affy GeneChip Mouse 430 2.0 Array.

Does anyone know where I can download genomic coordinates (chromosome, strand, start, end) for all probesets of this microarray? I was searching the Affy website for a couple of hours, can't find it. The microarray in question is:

Affymetrix GeneChip Mouse Genome 430 2.0 Array

Admittedly this is a very microarray-centric question, but the reason I'm asking is this: I want to check if genes detected by the microarray are also detected by HT-Sequencing (not RNA-Seq actually, but similar).

I.e. I want to know if genes detected by the microarray have also been detected by the HT-Sequencing. The question is just whether the same genes have been detected or not, NOT whether similar expression levels have been detected.

From the HT-Sequencing, I have coordinates of sequenced tags. I want to map them to some intermediate (RefSeq) and compare with expression levels from the probesets, which is data that I also have. Because directly comparing sequenced tags against probesets is not very informative I think.

Suggestions for alternative approaches are also very welcome.

Thanks.
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Old 04-11-2011, 02:55 AM   #2
ETHANol
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Location: Western Australia

Join Date: Feb 2010
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Default

With the R/Bioconductor package BiomaRt use this script

> library(biomaRt)
> ensembl = useMart("ensembl")
> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> affyids <- read.delim("mytextfile.txt", header=F,stringsAsFactors=F)[,1]
> genelocs <- getBM(attributes = c("chromosome_name", "start_position",
"end_position", "strand"), filters = "affy_hg_u133_plus_2", values = affyids, mart = ensembl)
#### you can also use "affy_hg_u133_plus_2", "hgnc_symbol" to get affy probe set and gene symbol. "mytextfile.txt" is a list of Affy probe sets and you need to change the filter to your gene chip.


> data.frame(genelocs)
> write.table(genelocs, file = "genelocs.bed", append = FALSE, sep = "\t")
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