Voom with QuSAGE

Question

[Colari19]

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.

Answer 1

[Gordon Smyth]

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.

[Colari19]

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