Affy Data Into Illumina Genome Studio

Question

[Biomed]

Hi, Does anyone know if and how I can get affymetrix chip data into Illumina genome studio for viewing and further analysis? Sorry for being vague but it shows my ignorance on this subject so please be patient. In our lab we use Illumina chips and the biomedical researcher who is analyzing these SNP chips has only worked with Illumina genome studio before. Neither he nor I have any prior experience with the good old Affy technology. We have a collaborator who wants to send us the data from Affy chips and have us analyze that data. Unfortunately the only platform we are comfortable doing this is the Genome studio software so even before I got a hold of that data I wanted to ask here for ideas.Thanks Thanks

[Sean Davis]

More details needed. What affy data type? What "viewing and further analysis" do you want to do? I venture to say that using Genome Studio for affy data is likely to be akin to the old "square peg in round hole".

[Biomed]

preferred_languages=['python']
if answer in preferred_languages:
     thanks=1
return thanks

[Andrew Su]

my guess is that if you added more information about what you wanted to accomplish (i.e., why you want to load data into Illumina GS), many people here would have suggestions on easier (and likely better) ideas on how to get it done.

[Andrew Su]

To follow on Sean's comment, my guess is that if you added more information about what you wanted to accomplish (i.e., why you want to load data into Illumina GS), many people here would have suggestions on easier (and likely better) ideas on how to get it done.

[Biomed]

Thanks guys and sorry for being vague but it shows my ignorance on this subject so please be patient. In our lab we use Illumina chips and the biomedical researcher who is analyzing these SNP chips has only worked with Illumina genome studio before. Neither he nor I have any prior experience with the good old Affy technology. We have a collaborator who wants to send us the data from Affy chips and have us analyze that data. Unfortunately the only platform we are comfortable doing this is the Genome studio software so even before I got a hold of that data I wanted to ask here for ideas.Thanks

[Istvan Albert]

Put the specifics into the main post (select the edit link and modify the post). You should specify what exactly is the data capture methodology platform, is it sequence capture, or some other method. Everything helps, if knowledge that you think is too simple. The more specific you are the easier is to assist you.

[Istvan Albert]

Put the specifics into the main post (select the edit link and modify the post). You should specify what exactly is the data capture methodology platform: is it sequence capture? tiling array? Everything helps, even knowledge that you think is too simple. The more specific you are the easier is to assist you.

[Biomed]

I think I will wait until I get the data in my computer and than I wil be able to ask more specific questions. Thanks anyway.

[Andrew Su]

What does "analyze that data" mean? SNP calling? copy-number analysis? something else?

Answer 1

[Neilfws]

I have not used Genome Studio, but I am sure that the answer to your question is "no". It is proprietary, designed specifically for Illumina platforms and distributed by Illumina - why would it import Affymetrix data?

If you are not familiar with R/Bioconductor, I suggest that you either become so quickly or find someone who is. It contains several packages which can process Affymetrix SNP chips (5.0 and 6.0): in particular, the packages crlmm and VanillaICE will perform genotyping and copy number estimation.

[Biomed]

I am familiar with R and Bioconductor but my colleague is not. And he wants to look at this data the way he is used to. That was the main motivation behind this question but thanks for the answer.

[Neilfws]

I see a lot of people who want to use "the tools that they are used to" (think excel instead of databases). The problem comes when those tools are inappropriate or worse, simply the wrong tool. When that happens it's time to learn a new tool, or defer to someone with the required experience.