how to get tissue name of cel files?
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@angelruvalkba-8251
Last seen 6.1 years ago
Mexico

 

I´m using bioconductor and I want to extract the tissue name of the cel files (not the file name itself because a lot of cel files with different names can be related to the same tissue) in order to create a principal component analysis scatter plot where each group name is equals to tissues names. I dont want to define every group manually but I dont know if there exists an attribute wich provides that information inside cel files.

I´m using oligo package. In the example image every cluster is a tissue and every dot is a cel file

 

pca oligo cel • 1.4k views
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@gabriel-nathan-kaufman-mr-4461
Last seen 6.1 years ago
Canada

I am not sure that you can obtain that information, unless the CEL file was generated in such a manner that it contains a specific annotation. Check the phenoData slot in the ExpressionSet object, because it might be there.

A helpful related thread:

Finding Annotation of CEL file formats

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