Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Affy Sues Illumina in genome-analysis and array technologies Digi Illumina/Solexa 7 07-14-2013 12:18 PM
Comparing mouse and human differentially expressed genes stephenhart General 3 11-16-2011 01:14 AM
Downloading all mouse genes and up/downstream seuences fahmida General 2 05-10-2011 03:25 AM
PubMed: Massively parallel sequencing of ataxia genes after array-based enrichment. Newsbot! Literature Watch 0 02-13-2010 02:10 AM
PubMed: Mutation discovery in the mouse using genetically guided array capture and re Newsbot! Literature Watch 0 07-25-2009 05:07 AM

Thread Tools
Old 04-11-2011, 12:07 AM   #1
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.

Azazel is offline   Reply With Quote
Old 04-11-2011, 01:55 AM   #2
Senior Member
Location: Western Australia

Join Date: Feb 2010
Posts: 308

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")
ETHANol is offline   Reply With Quote

affymetrix, comparison, microarray

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 09:05 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO