This is a test version of Biostars. For the public version, visit https://www.biostars.org.
What is the unit of TCGA RNA-seq data downloaded from cBioPortal?

Hi,

Many thanks in advance! I downloaded RNA-seq data of lung adenocarcinoma from cBioPortal: http://www.cbioportal.org/study?id=luad_tcga_pub#summary

This data includes the file entitled data_RNA_Seq_v2_expression_median.txt and my question is what is the unit of figures included in this file??

I checked the description about this file included in the downloaded data and also spent hours to figure out if it's RPKM, read count etc, but couldn't find a clue. Any comment would be greatly appreciated!!!

Thank you so much,

Amy

rna-seq
• 4,627 views • link
updated by Kevin Blighe Kevin Blighe • written by Amy • Amy

1 answer

...............................

• 0 views • link
written by Kevin Blighe Kevin Blighe

Hello Kevin,

Sorry for delay of response. Thanks so much!!!

Amy

• 0 views • link
written by Amy • Amy

Hello Kevin,

So can I directly use the data in data_RNA_Seq_v2_expression_median.txt to perform differential analysis or pathway enrichment analysis?

Thanks!

• 0 views • link
written by masicong.smu • masicong.smu

Hey, this thread is 2 years old. You may want to open a new question (and provide more details about the data that you're using).

• 0 views • link
written by Kevin Blighe Kevin Blighe

Log in to answer this question.

More posts like this
  • TCGA differential DNA methylation analysis 450K best practices
    written by Brassicka • Brassicka
    Hello, I am trying to do differential methylation analysis comparing matched tumor versus normal tissue from TCGA-LUAD. Essentially, I have tried doing it three different …
  • Tutorial: How to download GEO data Quickly and easily
    written by Novogene • Novogene
    Data mining is a popular area of bioinformatics analysis. In general, "mining" refers to the acts of retrieving and gathering information from vast amounts of …
  • GTF to match transcriptome data in TopHat
    written by blur blur
    Hi, I am trying to do risobome profilings, and to that end I have been trying to align reads to the human transcriptome with no …
  • Getting copy number variation from .CHP files for REMBRANDT study
    written by PleaseDeleteMe • PleaseDeleteMe
    Hi all, As a preface: I am not very familiar with genetics/genetics processing/bioinformatics as this is not normally the side of work I'm on. So …
  • Question about ClinicalData discrepancies b/w cbioportal data and GDC data?
    written by Vasu Vasu
    I recently downloaded the TCGA colorectal clinical data information from [GDC portal][1]. From this I got the following files. nationwidechildrens.org_clinical_patient_coad.txt nationwidechildrens.org_clinical_patient_read.txt I combined both the …
  • trying to reproduce heat map made via cBioportal using download data
    written by chrisclarkson100 chrisclarkson100
    I need to make a statistical comparison using breast cancer data. I have made a heat map at the following link on the Bioportal: http://www.cbioportal.org/index.do?cancer_study_id=brca_tcga&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&data_priority=0&case_set_id=brca_tcga_mrna&gene_list=BRCA1%250ABRCA2%250ATP53%250ACCL2%250ACCR3%250ACD44%250AENG%250AIL6%250AIL33%250ACD33%250ACSF1%250AHIF1A%250ACLEC7A&geneset_list=%20&tab_index=tab_visualize&Action=Submit&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=brca_tcga_mrna_median_Zscores&show_samples=false&heatmap_track_groups=brca_tcga_mrna_median_Zscores%2CBRCA1%2CBRCA2%2CTP53%2CCCL2%2CCCR3%2CCD44%2CENG%2CIL6%2CIL33%2CCD33%2CCSF1%2CHIF1A%2CCLEC7A …
  • MCP counter's problems
    written by Neil • Neil
    Hello. I need to produce analysis on this study http://www.cbioportal.org/study?id=skcm_tcga#summary I downloaded the datasets and among then found the file > data_RNA_Seq_v2_expression_median.txt Next I need …
  • Mutation processing by cbioportal
    written by Arnaud Ceol Arnaud Ceol
    Hi, I got lost with the mutations from TCGA made available from cbioportal (http://www.cbioportal.org/) and from the gdc portal (http://gdc-portal.nci.nih.gov/), and I've the feeling I'm …
  • Tutorial: Guide to TCGA data
    written by Jordan Anaya Jordan Anaya
    Guide to TCGA data ================== Hi, I've been working with TCGA data for a couple years now and I am the creator of OncoLnc. In …
  • Job: Manager - Lab Data Operations
    written by rhoffman • rhoffman
    Fred Hutchinson Cancer Research Center, home of three Nobel laureates, is an independent, nonprofit research institution dedicated to the development and advancement of biomedical research …