Question: Is there any way of exporting CNV data from Affymetrix SNP 6.0 arrays from Nexus Software for OncoScan?
0
gravatar for IOM
3.8 years ago by
IOM20
Birmingham
IOM20 wrote:

Hi everyone,

Thanks for reading. I am doing some work with Affymetrix SNP 6.0 arrays using NExus for OncoScan software. I would like to export the data in order to do some hierarchical clustering, heatmaps, correlation matrices, etc, but the only format I can get is a BED format (.BGR) , and it does not provide with the names of the samples, just coordinates, gains and loses. Does anybody have a better idea? Anything will be more than welcomed, thanks for your time.

 

Best regards

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by IOM20
Answer: Is there any way of exporting CNV data from Affymetrix SNP 6.0 arrays from Nexus
1
gravatar for James W. MacDonald
3.8 years ago by
United States
James W. MacDonald52k wrote:

This isn't a support site for NExus for OncoScan, so you would be better off asking Affy, or reading their documentation.

You could alternatively use the crlmm package to make your CNV calls, in which case you wouldn't have any problem with exporting data.

ADD COMMENTlink written 3.8 years ago by James W. MacDonald52k
Answer: Is there any way of exporting CNV data from Affymetrix SNP 6.0 arrays from Nexus
0
gravatar for IOM
3.8 years ago by
IOM20
Birmingham
IOM20 wrote:

Hi James,

Thanks for your reply. I already have spoken with a person from Affy, and has said that there is no possible way of exporting anything from Nexus, the analysis has to start from the CEL files. Do you know any tutorial (apart from crlmm) where I can learn how to perform a hierarchical clustering, heatmaps, and other tasks, as I already have done the calling with Nexus? That would be very helpful. Thanks again.

Best regards

IOM

ADD COMMENTlink written 3.8 years ago by IOM20

I'm not sure what you are asking. If you can't export anything from Nexus, what does it matter if you have done the calls using Nexus? It seems you need to go back to celfiles and make copy number calls using crlmm. Then you can do heatmaps or whatever.

As for tutorials, you could look at the vignettes for ComplexHeatmap. Making heatmaps is a very common thing to do, so a well crafted Google search is probably your best bet.
 

ADD REPLYlink written 3.8 years ago by James W. MacDonald52k

Hi James,

What I would to do is the hierarchical clustering and heatmaps, but without anything I can export from Nexus, I can not do it. That is why I wanted to start from the CEL files, not in order to get the CNV ( as I already have that from NEXUS) but for  getting a file with all the samples and events, and this way being able to perform the clustering. I will try what you say. Thanks

ADD REPLYlink written 3.8 years ago by IOM20
Answer: Is there any way of exporting CNV data from Affymetrix SNP 6.0 arrays from Nexus
0
gravatar for IOM
3.8 years ago by
IOM20
Birmingham
IOM20 wrote:

Hi James,

Thanks for your reply. I already have spoken with a person from Affy, and has said that there is no possible way of exporting anything from Nexus, the analysis has to start from the CEL files. Do you know any tutorial (apart from crlmm) where I can learn how to perform a hierarchical clustering, heatmaps, and other tasks, as I already have done the calling with Nexus? That would be very helpful. Thanks again.

Best regards

IOM

ADD COMMENTlink written 3.8 years ago by IOM20
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