This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Probe matching between HuEx-1_0-st-v2 and MoGene-1_0-st-v1

I want to compare data between affymetrix chips of human HuEx-1_0-st-v2 and mouse MoGene-1_0-st-v1. First step is I need to map probe id between these 2 arrays. Any suggestions?

microarray
• 3,044 views • link
updated by Ram Ram • written by justinzhang.xl • justinzhang.xl

Details on what these ids are would help you get a more relevant answer. Like, are they numbers? Where are they suited? In what format ate they stored? The more details, the more relevant our answers can be!

• 0 views • link
written by Ram Ram

The probe id for these 2 arrays are numbers.

Human one is :

Copyright 2005-2008, Affymetrix Inc.
All Rights Reserved

The content of Affymetrix array sequence files is covered by the
terms of use or license located at http://www.affymetrix.com/site/terms.affx

Array name:      Human Exon 1.0 ST
Array/chip type: HuEx-1_0-st-v2
Part Numbers:    900649, 900650, 900651, 900654
Organism:        Homo sapiens

This README provides a guide to the contents of the array sequence
files for the Affymetrix Human Exon Array.

Human Exon Array support materials web site:
http://www.affymetrix.com/support/technical/byproduct.affx?product=huexon-st

Mouse one is:

Copyright 2007-2008, Affymetrix Inc.
All Rights Reserved

The content of Affymetrix array sequence files is covered by the
terms of use or license located at http://www.affymetrix.com/site/terms.affx

Array name:      Mouse Gene 1.0 ST
Array/chip type: MoGene-1_0-st-v1
Part Numbers:    901168, 901169, 901171, 901178, 901179
Organism:        Mus musculus

This README provides a guide to the contents of the array sequence
files for the Affymetrix Mouse Gene Array.

Mouse Gene Array support materials web site:
http://www.affymetrix.com/support/technical/byproduct.affx?product=mogene-1_0-st-v1
• 0 views • link
updated by Ram Ram • written by justinzhang.xl • justinzhang.xl

1 answer

I don't think you can compare probe IDs against two different arrays from two different species. What you can do thought is to use BioMart to find the correspondence between the human probe IDs (FILTERS) and HGNC genes (ATTRIBUTES) and then their mouse orthologues (ATTRIBUTES). And you can do the same for mouse: find the MGI symbols (ATTRIBUTES) mapped to the mogene array (FILTERS) and get the human orthologues if you wish.

• 0 views • link
updated by Ram Ram • written by Denise CS Denise CS

From the page http://www.affymetrix.com/support/technical/comparison_spreadsheets.affx#1_3

You could find there are comparisons of across species between arrays.

  • Mouse Expression 430 to Human Genome U133 Plus 2.0 Array

Within species between arrays: http://www.affymetrix.com/support/technical/comparison_spreadsheets.affx#1_2

  • Human Genome U133 Plus 2.0 Array to Human Exon 1.0 ST Array
  • Mouse Gene 1.0 ST to Mouse Expression 430 Array

These comparisons were generated by Affymetrix, but they are not generating any more. What I need is the comparison between Human Exon 1.0 ST Array and Mouse Gene 1.0 ST, which is not there.

Therefore, I am looking for any open sources tools to match probe ids of these 2 arrays. Any suggestions?

• 0 views • link
updated by Ram Ram • written by justinzhang.xl • justinzhang.xl

Log in to answer this question.

More posts like this