Question: What is the best way to quantile normalize expression matrix ?
0
gravatar for jack
5.4 years ago by
jack790
Germany
jack790 wrote:

I have an expression matrix, its rows belong to different genes and columns belong to samples.

I want to do quantile normalization. But for me seems two ways to normalize it. First: row wise; normalize the expression of  every gene in all samples. Second: normalize columnwise: normalized expression of all genes in one sample and then go to other sample and ....

 

Which one makes more sense?  

ADD COMMENTlink modified 2.0 years ago by DataFanatic140 • written 5.4 years ago by jack790
4
gravatar for Devon Ryan
5.4 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

The point of quantile normalization is to make the signal distribution of the samples as close as possible, so you normalize the columns. Trying to normalize the rows would introduce a whole host of issues that could seriously muck with the results (e.g., since you look for differential expression across rows, how might normalizing each row affect that...).

ADD COMMENTlink written 5.4 years ago by Devon Ryan92k

Good point Devon. I'm using normalize.quantiles(x,copy=TRUE) to do quantile normalization, but they didn't explain that, it's normalize by row or column. do you know useful function for quantile normalization?

ADD REPLYlink modified 11 weeks ago by RamRS24k • written 5.4 years ago by jack790

The only other one that I know of off-hand (aside from tweaked versions, like cqn) is normalizeBetweenArrays() from the limma package. I wouldn't be surprised if there are others.

ADD REPLYlink modified 11 weeks ago by RamRS24k • written 5.4 years ago by Devon Ryan92k
0
gravatar for  DataFanatic
2.0 years ago by
DataFanatic140
DataFanatic140 wrote:

Thank you very much for answering this question Devon, I have a follow-up question: Under what circumstances is it appropriate to do both log transformation and quantile normalization? Thank you in advance.

ADD COMMENTlink written 2.0 years ago by DataFanatic140
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1965 users visited in the last hour