Bioconductor package NOISeq: Normalization

Question

[KVC_bioinfo]

Hello All, I am using the NOISeq package for normalization of RNA-seq data. From the following link:

Package

I am not able to understand what "long" signifies here? rpkm(datos, long = 1000, lc = 1, k = 0)

from the explanation in the document, it says feature length. I am I am not sure what exactly it means. Could someone help me out? Thank you in advance.

[jared.andrews07]

You'd probably have better luck on the Bioconductor support site. The package maintainers likely frequent that forum.

Answer 1

[Kevin Blighe]

It relates to the fragment length: What is the difference between a Read and a Fragment in RNA-seq?

In RNA-seq normalisation, it is possible (and recommended) to adjust for fragment length biases.

You should be able to determine this for each of your transcripts if you have a BED/GTF/GFF file.

Kevin

[KVC_bioinfo]

Thank you! It is very helpful.