FPKM without normalization
1
0
Entering edit mode
8 weeks ago
maryak ▴ 20

Can i a use gene expression RNAseq FPKM data provide in https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Breast%20Cancer%20(BRCA)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443 for classification of metastasis and non metastasis sample without normalization?

FPKM classification Normalization • 348 views
ADD COMMENT
6
Entering edit mode
7 weeks ago
ATpoint 87k

Nobody can tell you because you do not say that exactly your strategy is. Generally, FPKM is a normalized unit, but it has been shown many times before that plain FPKM, that is correction only for depth (but not composition) and length might underperform if there are a lot of DEGs between groups. Here is a writeup from the past explaining plain library size vs something more sophisticated: TMM-Normalization

A great view for what composition bias is: See StatQuest

ADD COMMENT

Login before adding your answer.

Traffic: 1722 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6