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titlePatch: October 2016

The LIHC RPPA data submitted by MDACC were discovered to be mislabelled MESO samples. The analyses and standard data pipelines for LIHC have been re-run using the corrected samples submitted in March, and the nozzle reports now contain notices of the discrepancies.

 

The following table shows the changes in sample counts for RPPA data as a result of this patch:

HNSC

+145

(357 total)

LIHC

+121

(184 total)

THCA

+146

(368 total)

 

Anchor
2016_01_28

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titleJanuary 2016 data run
  1. Summary of sample changes (see the comprehensive samples report for more details):

    Clinical

    +8

    (11196 total)

    MAF

    +122

    (7099 total)

    mRNASeq

    +214

    (10267 total)

    rawMAF

    +1576

    (6322 total)

    RPPA

    +626

    (7429 total)

  2. Significant changes to clinical data processing, to accommodate new XSD 2.7 format adopted by TCGA:
    1. Per TCGA this new format is not backwards compatible with the previous XML, so if you use a parser customized to the previous XSD, it may not work correctly.  This change is confined to the XML, no other TCGA data is affected by this change.
    2. These changes are detailed at https://wiki.nci.nih.gov/display/TCGA/Release+1.39.1#Release1.39.1-XSD2.7Implementation
    3. In the new format, 'CQCF' parameters are removed. Instead, they are provided in new XML format, SSF.
    4. According to this change, 'cqcf' parameters are removed and "patient.tumor_samples" and "patient.normal_controls" parameters are added in the clinical merged data. 
    5. Added parameters of two new XML formats, OMF and SSF in the clinical merged data 
  3. Fix a bug in Methylation_Preprocess that caused duplicate entries in methylation data
  4. Added outlinks to TCGA Encyclopedia to the About and Documentation menus of the Broad GDAC Firehose website
  5. FireBrowse v1.1.24:
    1. Loaded this data run
    2. Numerous internal updates to further simplify deployment, which e.g. will help provision AWG-specific databases
    3. The HeartBeat API function now includes: the directory from and time at which the API server was launched
    4. Dropped beta clause from version

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title2013_12_10 (December 2013)
  • Summary of sample changes (see the comprehensive samples report for more details):

    BCR

    +221

    (9165 total)

    Clinical

    +129

    (7509 total)

    CN

    +57

    (8277 total)

    LowP

    +179

    (1038 total)

    MAF

    +313

    (5006 total)

    Methylation

    +469

    (8514 total)

    miRSeq

    +107

    (7391 total)

    mRNASeq

    +93

    (7350 total)

  • New/Updated MAFs:
    • ACC (90 samples)
    • LAML (55 new samples)
    • PRAD (168 new samples)
  • New archives were uploaded by UNC to address GBM miRNAseq issue reported last month (2013_11_14 stddata run)
  • Part 1 of 2 major upgrades to the Broad GDAC website: be sure to flush your cache to see the new layout
  • Part 2 will be available with the next analysis run release, converging the stddata and analysis dashboards into a single, integrated entity

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title2012_08_25

  • Dicer:
  • Gene annotated protein expression data (RPPA) are now available for LUSC, LUAD, and HNSC.
  • New SARC disease type reflected (Sarcoma)
  • Sample Changes

    CN

    +323

    (5810 total)

    Clinical

    +31

    (5671 total)

    LowP

    +402

    (478 total)

    Methylation

    +7

    (5471 total)

    RPPA

    +407

    (2731 total)

    mRNA

    +7

    (2224 total)

    mRNAseq

    +29

    (3527 total)

    miR

    +7

    (1061 total)

    miRseq

    +20

    (4109 total)

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