Question: Where Can I Find A Coordinates (Genomic Coordinates For Probes) File For Affymetrix Data ?
1
gravatar for Wayne
6.9 years ago by
Wayne1000
United States
Wayne1000 wrote:

Hello all, I am trying to utilize the microarray data found here http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6338

The data used the [HG-U133Plus2] Affymetrix Human Genome U133 Plus 2.0 Array. I've come to the point where I need a coordinates file which has information about the genomic coordinates for the microarray probes, to add locus information to the .CEL files so that they can be combined with RNAseq data. Does anyone know how to go about getting this file. Is it platform specific or experiment specific? I am very new to this so please bare with me!

Thanks

ADD COMMENTlink written 6.9 years ago by Wayne1000
2
gravatar for Ryan D
6.9 years ago by
Ryan D3.3k
USA
Ryan D3.3k wrote:

Yes, you can find them all at the Affymetrix website: http://www.affymetrix.com/support/technical/byproduct.affx?cat=arrays&Human#Human. Your particular array data is under the section 3' Gene Expression Analysis Arrays -> Catalog Arrays -> Human Genome U133 Plus 2.0 Array .

The direct link to the library files--which appears to be what you need--is here: http://www.affymetrix.com/Auth/support/downloads/library_files/hgu133plus2_libraryfile.zip

ADD COMMENTlink written 6.9 years ago by Ryan D3.3k

Thank you for your response. I downloaded the linked lib files you provided... but in the folder I don't see any files that have probe identifier, chromosome, start, end, probe length . That is the information that I need. I found this file --- >http://www.affymetrix.com/Auth/analysis/downloads/na29/ivt/HG-U133A_2.na29.annot.csv.zip Which looks like it might have this information in the " alignments column" but the lengths of the regions are way too large to be probe lengths right ? What do you think ?

ADD REPLYlink written 6.9 years ago by Wayne1000
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