How to perform differential expression analysis without the matched normal tissue data?
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11 weeks ago
Zahra ▴ 20

Hi all,

I want to analyze the differential expression of my interest genes. For this aim, I want to use the PCAWG data, but As far as I have searched, most of the patients don't have the matched normal tissue data. I would be appreciated if you help me with how to find the matched normal expression data of the PCAWG. If the normal tissue data is not available, does it correct to perform DE analysis without them?

Thanks for any help

RNA-Seq Differential Expression DE ICGC PCAWG • 218 views
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If there are no matched normals (which is probably the case) then there is no DE analysis unless you define subclusters in your data and compare between these. Be aware though that these consortium datasets have been used and published dozens if not hundreds of times (incl definition of subclusters and its DE) so be sure that what you aim to do is novel and genuine to not waste time reinventing the wheel.

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