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UCSC Xena

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 by genome-cancer

Suggested by: Roy Granit

Description

A web-based exploration tool for public and private, multi-omic and clinical/phenotype data.

Questions Xena can help you answer:
Is over-expression of geneA associated with lower survival?
Is geneB differentially expressed in tumor vs normal?
Do my subgroups have differential survival?
What is the relationship between expression, mutation, copy number, etc for these genes?

What sets us apart:
View your data, public data or both. Secure and easy. Mac, Windows, Linux
Non-coding and coding regions
All types of expression: mRNA, miRNA, protein, lncRNA exon, transcript, and more
Genomic Signatures

Discussion

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Aurel Anzinger
Undergraduate at Ludwig Maximilian University of Munich
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Aurel Anzinger

Undergraduate at Ludwig Maximilian University of Munich

difference between log2 (norm_value+1) and log2 (norm_count+1) in Xenabrowser Dataset Oval 17

Hi there!

At the time i´m working with downloaded Datasets of the Xenabrowser; Expressiondata of Chemokines, on the on Hand derived from the TCGA Dataset and on the other hand derived from the Target-TCGA-Gtex Dataset!
As it came to my knowledge, when i was about to plot them in Graphpad Prism on my own, the Data log2 (norm_value 1) shifts compared to the Data normalised log2(norm_count 1). Does anybody know what´s the difference between those two normalizations? Are there differences or is it just mathematically? Thanks for your help

Best,
Aurel

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Posted: 7 months ago
Roy Winters
Research Fellow at University of Melbourne
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Roy Winters

Research Fellow at University of Melbourne

@Aurel.Anzinger.834:u I believe that the 'count' option refers to the raw counts, while 'norm means normalized counts (meaning the data was normalized to allow comparison between samples)

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Posted: 6 months ago
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