Quartile Normalization in R : RNA-seq

Question

[KVC_bioinfo]

Hello,

I am trying to use quartile normalization in R. I came across This lib. However, I could not load it. Is there any other away to do quartile normalization in R?

Answer 1

[amyloid.beta.martin]

https://bioinformatics.stackexchange.com/questions/2586/how-to-apply-upperquartile-normalization-on-rsem-expected-counts

[Kevin Blighe]

I guess that this thread is sequentially linked to this: Quantile Normalization in R

[KVC_bioinfo]

Is it the same thing? I am confused if quartile normalization and quantile normalization are same?

[Kevin Blighe]

My apologies. It's late here and my eyes are almost closed. I did not see the different 'r' (quartile) and 'n' (quantile). They are different

[KVC_bioinfo]

No worries. I am trying to find how quartile normalization is done in R?

[Kevin Blighe]

Quartile and quantile are performed differently. Quantile (with 'n') became very popular in microarray analysis, as you probably know. I have not seen quartile (with 'r') used that much; however, in RNA-seq, 'upper quartile' is a method that is used for normalisation.

There is material on the WWW that discusses this, such as: Which method should you use for normalization of RNA-Seq data?

[KVC_bioinfo]

Thank you. Are you aware of any R package for doing this? (Quartile)

[Kevin Blighe]

Hello again Sir, well, quartiles are just quartiles (data range divided into 4). To use them for normalisation requires the use of one of the quartiles, such as in upper quartile normalisation. I have not had to do this in R previously, but this function appears valid: https://www.rdocumentation.org/packages/NOISeq/versions/2.16.0/topics/Normalization

This is, for example, used for some of the TCGA data: https://gdc.cancer.gov/about-data/data-harmonization-and-generation/genomic-data-harmonization/high-level-data-generation/rna-seq-quantification

[KVC_bioinfo]

Best!! Let me try this out. Thanks!