Frequently Asked Questions (FAQ)

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About the project

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  How many samples are processed for each cancer?
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  What is the difference between the TCGA pilot project and the current TCGA project?
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  Why did you choose MAGE-TAB over other formats to model data?

About the data

Data Access

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  How do I download clinical data for specific disease study?
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  My password no longer works for downloading Controlled Access data?
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  Why are some TCGA data protected and how can I gain access to them?

Data Identification

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  Do you have a summary table of all the samples processed?
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  How do I determine what kind of tissue was used for a sample using the TCGA Barcode?
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  How do I read a TCGA barcode?
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  Is the normal always an adjacent normal for each cancer?
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  What are the different levels of data and what do they mean?
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  What does a portion code represent?
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  What is a batch?
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  What is a sample code?
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  What is the difference between a tissue slide and a diagnostic (FFPE) slide?

Data Availability

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  How can I find Copy Number data for the SNP platforms using the Data Matrix?
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  How do I retrieve results for samples that are available on all platforms?
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  In the Data Matrix, what do A (Available), N (Not Available), P (Pending) and blank (Not Applicable) mean?
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  In the Data Matrix, why are there 'Not Available' and 'Available' data for a single batch?
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  In the Data Matrix, why are there large areas of 'Not Applicable' spaces for some sample-platform combinations?
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  In the Data Matrix, why do some samples only have clinical data?
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  Is the normal always an adjacent normal for each cancer?

Data Submission

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  Can I contribute results for a cancer that is not listed on the TCGA Portal?
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  I need to have data removed from the TCGA repository and website
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  I've created (or will be submitting) a new data type
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  I've created (or will be submitting) a new file format
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  I've developed some analysis tools that I want to make available to the TCGA community. How can I have them hosted?
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  I've just purchased a new instrument. How do I know if TCGA can accept my data?
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  My institute would like to contribute to TCGA, what do I need to do?
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  This is my first time submitting data, what do I need to do?
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  We're publishing a paper using TCGA Data. Can we publish the data on the TCGA Portal?

Data Quality

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  I have a question or problem with TCGA data. Who should I contact?
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  I need to have data removed from the TCGA repository and website
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  Is the normal always an adjacent normal for each cancer?

Annotations

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  Where can I get the marker file for Affymetrix SNP 6 data?
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  Where can I obtain a CDF file that was used in GBM or OV analyses?
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  Where does the reference allele for a MAF file come from?

Data Format

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  For DNA Methylation data, why do you only report one beta value instead of two?
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  I've created (or will be submitting) a new file format
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  What are the different levels of data and what do they mean?
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  What is the difference between the MAF headers named “Verification_Status” and “Validation_Status” in describing somatic mutation status?
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  Where can I find a description of the Data Matrix column headers?
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  Why did you choose MAGE-TAB over other formats to model data?

Clinical Data

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  Biospecimen and Clinical XSD Files Specification - v2.5
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  How are XSDs versioned?
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  How do I download clinical data for specific disease study?
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  In the Data Matrix, why do some samples only have clinical data?
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  What are the 'days_to' values in clinical XML and biotab files?
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  What does the procurement_status attribute indicate?
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  What is the difference between a tissue slide and a diagnostic (FFPE) slide?
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  Which clinical common data elements (CDEs) are protected?

Mutation Annotation Files (MAFs)

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  Is the absence of a mutation in MAF file sufficient to call the individual wild type at that site?
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  What is an independent or orthogonal genotyping method in MAF files?
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  What is the difference between the MAF headers named “Verification_Status” and “Validation_Status” in describing somatic mutation status?
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  Where does the reference allele for a MAF file come from?

About the TCGA Portal

General portal questions

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  Can I contribute results for a cancer that is not listed on the TCGA Portal?
• Page:
  Do you have a summary table of all the samples processed?
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  For expression data, what is the difference between the values submitted to TCGA and ICGC?
• Page:
  How many samples are processed for each cancer?
• Page:
  I need to have data removed from the TCGA repository and website
• Page:
  I've created (or will be submitting) a new data type
• Page:
  I've developed some analysis tools that I want to make available to the TCGA community. How can I have them hosted?
• Page:
  I've just purchased a new instrument. How do I know if TCGA can accept my data?
• Page:
  My institute would like to contribute to TCGA, what do I need to do?
• Page:
  We're publishing a paper using TCGA Data. Can we publish the data on the TCGA Portal?
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  What are the Analytical Tools?

Data Reports

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  Do you have a summary table of all the samples processed?
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  How do I determine what kind of tissue was used for a sample using the TCGA Barcode?
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  What is the difference between the BAM Telemetry Reports and the BAM Telemetry Files?
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  Why are some TCGA data protected and how can I gain access to them?

Biospecimen Metadata Browser (Application)

• Page:
  Do you have a summary table of all the samples processed?
• Page:
  How many samples are processed for each cancer?
• Page:
  Is the normal always an adjacent normal for each cancer?
• Page:
  What is a batch?

Data Matrix (Application)

• Page:
  Do you have a summary table of all the samples processed?
• Page:
  How can I find Copy Number data for the SNP platforms using the Data Matrix?
• Page:
  How do I download clinical data for specific disease study?
• Page:
  How do I retrieve results for samples that are available on all platforms?
• Page:
  In the Data Matrix, what do A (Available), N (Not Available), P (Pending) and blank (Not Applicable) mean?
• Page:
  In the Data Matrix, why are there 'Not Available' and 'Available' data for a single batch?
• Page:
  In the Data Matrix, why are there large areas of 'Not Applicable' spaces for some sample-platform combinations?
• Page:
  In the Data Matrix, why do some samples only have clinical data?
• Page:
  My screen size is small, and I can't see the vertical scrolling control for the Data Matrix. How can I fix this?
• Page:
  What are the different levels of data and what do they mean?
• Page:
  What is a batch?
• Page:
  Where can I find a description of the Data Matrix column headers?
• Page:
  Why are some TCGA data protected and how can I gain access to them?

Bulk Download (Application)

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  If this is Bulk Download, why can I only download one archive at a time?
• Page:
  Why are some TCGA data protected and how can I gain access to them?

Data Browser (Application)

• Page:
  For DNA Methylation data, why do you only report one beta value instead of two?