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Question: How to compare RNA-seq counts matrices from different aligners ?
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gravatar for Aurora
4 months ago by
Aurora10
Aurora10 wrote:

I have used an aligner to produce raw counts from a publicRNA-seq data (GSE63310 , the counts are available online). I would like to compare my results with the "official ones" on the GEO website but I don't know how to compare accurately these two matrices to have an idea of their similarity.

Thank you for advices

ADD COMMENTlink written 4 months ago by Aurora10

Are they in the same id name? Are they for the same sample? Then you can do a PCA for each matrix, and compare the results. Are the same samples near the same other samples?

ADD REPLYlink written 4 months ago by LluĂ­s R370
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