Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Using GEO data as a Custom Track in UCSC Genome Browser A_Harrington Bioinformatics 1 12-10-2013 01:04 PM
is is possible to visualize RNA-seq data in UCSC genome browser(ENCODE)? HSV-1 RNA Sequencing 5 07-21-2012 06:24 PM
Adding NGS data to the UCSC genome browser aer General 18 06-27-2011 06:43 AM
RNA-Seq: ENCODE whole-genome data in the UCSC genome browser (2011 update). Newsbot! Literature Watch 1 11-24-2010 01:08 PM
aggregating data for features using UCSC Table Browser M.N. Bioinformatics 0 05-17-2010 12:02 PM

Thread Tools
Old 01-21-2019, 11:41 AM   #1
Junior Member
Location: London

Join Date: Jan 2019
Posts: 1
Default Normalisation of RNAseq data from UCSC Xena Browser

Dear all

I am very new to this so apologies in advance..

I am trying to teach myself the basics of R and bioinformatics and would like to attempt some analysis of TCGA data

I have downloaded the RNA-seq data from the LUAD TCGA data set using the 'HTSeq-Counts' link from this page:

I would like just do a simple correlation of expression of gene y with gene z

I then want to perform Kaplan-Meier analysis of overall survival after dividing patients into high and low expression of gene y (using the median to split the cohorts)

My questions are about normalising the data, before I perform the analyses

1) The UCSC page explains that the data has been log(x+1) transformed. I would like to know if the raw data was normalised for library size prior to log transformation? If not, is this necessary?

I obtained the count matrix and back-transformed the counts ((2^x) - 1) and I then summed the total counts per sample and obtained different values per sample, which makes me assume that the counts were not corrected for library size

2) Finally, assuming that the data have not been normalised for library size (or distribution etc) what method would you suggest to normalise for my analysis. I understand I could just do TPM or could do TMM or another method such as that used by DESeq2

Thanks in advance for any help, I did try to find the answer to q1 elsewhere but couldn't
sam007 is offline   Reply With Quote

normalisation, rna-seq advice, tcga, xena

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 11:53 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO