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Voom with QuSAGE

Hi,

Does anyone know if voom-normalised counts are compatible with QuSAGE, or should I just use the edgeR cpm function to get log2 expression counts?

I'd rather use voom for consistency across my different analyses, but I'm not sure if the precision weights pose a problem for QuSAGE...

Thank you.

rna-seq qusage limma voom r
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updated by Gordon Smyth Gordon Smyth • written by Colari19 Colari19

1 answer

qusage() doesn't seem to use precision weights, and that would indeed be a problem if used on the output from voom().

You could use camera() however, which does use precision weights, and which is much less conservative now than when the QuSAGE paper was published.

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written by Gordon Smyth Gordon Smyth

Thank you for your answer! I'll try CAMERA instead.

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written by Colari19 Colari19

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