Question

Is there any way of exporting CNV data from Affymetrix SNP 6.0 arrays from Nexus Software for OncoScan?

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IOM ▴ 20

@iom-7548

Last seen 7.7 years ago

Birmingham

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

cnv nexus for oncoscan Affymetrix 6.0 .BGR • 1.8k views

ADD COMMENT • link 8.8 years ago IOM ▴ 20

score 1 · Answer 1 · 2016-02-08

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 2 hours ago

United States

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 COMMENT • link 8.8 years ago James W. MacDonald 67k

score 0 · Answer 2 · 2016-02-09

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IOM ▴ 20

@iom-7548

Last seen 7.7 years ago

Birmingham

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 COMMENT • link 8.8 years ago IOM ▴ 20

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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 REPLY • link 8.8 years ago James W. MacDonald 67k

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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 REPLY • link 8.8 years ago IOM ▴ 20

score 0 · Answer 3 · 2016-02-09

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