TCGA COAD Expression data

Posted in TCGA data on the CGC by Asfand Yara Wed Jan 30 2019 13:17:27 GMT+0000 (Coordinated Universal Time)·4·Viewed 272 times

I have download TCGA COAD expression data file which have data like shown below. How these values are calculated and what does means by these values. Hybridization REF TCGA-AA-A00E-01A-01R-A002-07 Composite Element REF log2 lowess normalized (cy5/cy3) collapsed by gene symbol ELMO2 -0.201 CREB3L1 2.3005 RPS11 -0.080375 PNMA1 -1.23175
Aleksandar Jovic
Feb 1, 2019

Hello,

To assist you in your analysis, we would need a file access and information what was the query.

We suggest you to go through following page
https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/
that might be helpful for figuring out what these values present.

If you need further help, you can contact us at support@sbgenomics.com

Asfand Yara
Feb 3, 2019

I have downloaded the file named "US82800149_251976011133_S01_GE2_105_Dec08.txt_lmean.out.logratio.gene.tcga_level3.data" from GDC legacy portal which have the data as shown above.

Asfand Yara
Feb 3, 2019

And query was : Program Name IS TCGA AND Project Id IS TCGA-COAD AND Data Category IS Gene expression AND Data Type IS Gene expression quantification AND Experimental Strategy IS Gene expression array

Aleksandar Jovic
Feb 6, 2019

Hi,
Since Seven Bridges team did not perform calculations presented in TCGA files, our suggestion is to try finding information about experimental protocols and calculation methods in the following documentation.
These data are included in the MAGE-TAB archive.
https://docs.gdc.cancer.gov/Encyclopedia/pages/MAGE-TAB/
Hope this is helpful.

  
Markdown is allowed