Hi, I was trying to compare the normalization result from "qsmooth" and "quantile".
"qsmooth" works perfectly; however, I cannot get the correct result from quantile normalization.
Here's the code that I used:
data(skin)
skin <- normalizeTissueAware(skin, "SMTSD", "quantile")
assayData(skin)$normalizedMatrix # Return a matrix full of NA
Hi, I was trying to compare the normalization result from "qsmooth" and "quantile". "qsmooth" works perfectly; however, I cannot get the correct result from quantile normalization.
Here's the code that I used:
and the session info:
I quickly go through the source code, I think maybe the problems lies in line 46 of normalizeTissueAware.R
Maybe it should be change to something like:
Could you please help me take a look at this issue? Thank you very much for your time.
Best, Ping-Han