This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Getting The Cdf Files For Some Chip

Hi all,

I have some probe set data and I want to get the corresponding gene id for that. I have two types of chips

HG-U133Plus2 and HG-U133A and I want to get the CDF files for them so that I can get the corresponding gene id from the probe set id. I searched for a while but couldn't get it. Any suggestions?

Actually, I downloaded the files HG-U133Plus2 and HG-U133A(CDF and GIN) from the link http://www.findthatzipfile.com/search-44166747-hZIP/winrar-winzip-download-rlink315.zip.htm

However in matlab when I tried to read the corresponding Gene it using

  • cdfStruct=affyread('HT_HG-U133A.cdf');
  • probesetlookup(cdfStruct,'396fat')

I get the following results

  • Identifier: 'X97671 '
  • ProbeSetName: '396fat'
  • CDFIndex: 21990
  • GINIndex: 62
  • Description: 'X97671 /FEATURE=cds /DEFINITION=HSERYTHR H.sapiens mRNA for erythropoietin receptor'
  • Source: ''
  • SourceURL: ''

As you can see it doesn't give the Source and Source URL.

I was expecting something like this http://www.mathworks.com/help/bioinfo/ref/probesetlookup.html

gene-expression
• 4,052 views • link
updated by Biostar Biostar • written by mtyler.jason • mtyler.jason

1 answer

At the Affymetrix product page of Human Gene expression arrays tab technical documentation you will find all the files you need.

• 0 views • link
written by Irsan Irsan

I have added some updates. Can you please check?

• 0 views • link
written by mtyler.jason • mtyler.jason

I have made some updates in the question. Please anyone have a look and provide me valuable feedback

• 0 views • link
written by mtyler.jason • mtyler.jason

Have you tried one of the CDF's from affy's product page?

• 0 views • link
written by Irsan Irsan

Log in to answer this question.

More posts like this